Participant characteristics
The participants in the meta-analysis of GWAS for PUFAs included 1,454 HIS and 2,278 AFA unrelated participants (Table 1; fatty acid levels are expressed as the percentage of total fatty acids throughout the entire manuscript). There were some differences in the distributions of fatty acid levels observed across cohorts, which were likely due to the sources of biospecimens for the assays (plasma phospholipids for MESA and CHS versus erythrocytes for FHS). For example, mean levels of DPA varied from 0.85% (CHS: plasma phospholipids) to 2.54% of total fatty acids (FHS: erythrocytes) in AFA and AA from 11.01% (MESA: plasma phospholipids) to 16.56% (FHS: erythrocytes) in HIS (Table 1). In addition, n-6 PUFAs, especially LA and AA, have relatively higher mean levels than n-3 PUFAs in all cohorts (Table 1).
Table 1
CHARGE cohorts descriptives
| MESA/Hispanic Americans | FHS/Hispanic Americans | MESA/African Americans | CHS/African Americans | FHS/African Americans |
Participant characteristics | | | | | |
No. subjects | 1243 | 211 | 1472 | 603 | 203 |
Women | 629 (50.6) | 129 (61.1) | 788 (53.5) | 390 (64.7) | 130 (64.0) |
Age, years | 61 [53, 69] | 53 [44, 60] | 63 [53, 70] | 74 [71, 79] | 58 [50, 67] |
n-3 Polyunsaturated Fatty Acids | | | | | |
ALA (% of total fatty acids) | 0.16 [0.12, 0.20] | 0.21 [0.16, 0.27] | 0.15 [0.12, 0.19] | 0.13 [0.11, 0.17] | 0.18 [0.15, 0.23] |
EPA | 0.53 [0.37, 0.74] | 0.57 [0.47, 0.78] | 0.68 [0.51, 0.98] | 0.53 [0.39, 0.67] | 0.68 [0.48, 1.01] |
DPA | 0.86 [0.73, 1.00] | 2.49 [2.13, 2.79] | 0.93 [0.80, 1.07] | 0.85 [0.75, 0.97] | 2.54 [2.25, 2.89] |
DHA | 2.96 [2.29, 3.77] | 4.21 [3.45, 5.13] | 4.05 [3.25, 4.95] | 3.46 [2.87, 4.17] | 5.23 [4.21, 6.47] |
n-6 Polyunsaturated Fatty Acids | | | | | |
LA | 20.92 [18.87, 23.07] | 14.32 [12.24, 16.76] | 18.88 [17.12, 20.84] | 17.84 [16.46, 19.40] | 12.53 [10.88, 15.16] |
GLA | 0.11 [0.08, 0.14] | 0.15 [0.10, 0.18] | 0.10 [0.08, 0.13] | 0.07 [0.05, 0.09] | 0.10 [0.07, 0.15] |
DGLA | 3.57 [3.04, 4.13] | 1.95 [1.63, 2.35] | 2.89 [2.47, 3.33] | 2.76 [2.39, 3.24] | 1.51 [1.32, 1.78] |
AA | 11.01 [9.37, 12.84] | 16.56 [15.17, 17.74] | 13.21 [11.65, 14.82] | 12.64 [11.57, 13.86] | 17.17 [15.95, 18.48] |
Table 1 shows the participant characteristics of the Hispanic Americans and African Americans from each cohort (MESA, CHS and FHS). Data are presented as n (%) for binary measures or median [IQR] for continuous measures. Summary statistics are reported for the subset of individuals with data available for at least one of the fatty acid traits examined in genetic analyses. Fatty acids were measured in plasma phospholipids in MESA and CHS and in erythrocytes in FHS.
Regardless of whether the fatty acids were measured in plasma phospholipids or erythrocytes, AFA populations had higher levels of AA and elevated ratios of AA to DGLA and AA to LA relative to Hispanic populations. This result would be expected given the frequency differences in the derived (efficient) to ancestral (inefficient) FADS haplogroups between these two populations. As expected, due to the lower levels of dietary ALA relative to LA entering the biosynthetic pathway, levels of n-3 LC-PUFAs including EPA, DPA and DHA were significantly lower than the n-6 LC-PUFA, AA. Additionally, African Americans had higher levels of n-3 LC-PUFAs than Hispanic Americans, again likely due to differences in the ratio of the derived to ancestral FADS haplogroups. These differences are similar to those observed examining the same PUFAs and LC-PUFAs and ratios when comparing African Americans and European Americans.15,29
Confirmation Of Top Variants Identified In Prior Charge Eur Gwas Of Pufas
We began by examining associations of seven known PUFA-associated signals from CHARGE EUR in our current study of CHARGE HIS and AFA. Multiple variants identified by previous CHARGE EUR GWAS meta-analyses were also identified in CHARGE HIS (FADS1/2 region: rs174547 and rs174538, PDXDC1 variant: rs16966952 and GCKR variant: rs780094) and AFA (FADS1/2 region: rs174547, PDXDC1 variant: rs16966952, GCKR variant: rs780094 and ELOVL2 variant: rs3734398) after adjusting for multiple testing for the number of variants examined across the eight PUFAs (P < 0.05/8 = 0.006) (Table S1). The directions of effect observed in HIS and AFA for these variants were consistent with those reported for European ancestry populations in prior CHARGE GWAS meta-analyses of n-3 and n-6 PUFAs (Table S1).
Gwas And Fine-mapping Identify Novel Pufa-associated Genetic Signals In Charge His And Afa
Based on a genome-wide significance threshold of P < 5 x 10− 8, our complete GWAS of n-3 and n-6 PUFAs identified associations on chromosomes 11, 15 and 16 in CHARGE HIS (Table 2) and chromosomes 6, 7, 10 and 11 in CHARGE AFA (Table 3). For regions with more than one genome-wide significant variant, we applied statistical fine-mapping to identify the independent putative causal signals (credible sets) for each genome-wide significant locus. We carried out these analyses separately for our CHARGE HIS and CHARGE AFA GWAS meta-analysis results.
Table 2
Genome-wide significant signals (Credible sets) for PUFAs in CHARGE Hispanic Americans.
| Variants (Chr:Pos:EFF:OTH) | EAF | Zscore | Pvalue | Cluster | # Of SNP | Novel/ Known | Nearest Gene |
AA | rs102274 (11:61557826:C:T) | 0.506 | -24.26 | 5.1E-130 | 1 | 7 | Known | TMEM258 |
rs142068305 (11:67065755:T:G) | 0.196 | -7.06 | 1.63E-12 | 2 | 1 | Novel | ANKRD13D |
rs28364240 (11:67120530:G:C) | 0.204 | -7.04 | 1.88E-12 | 3 | 1 | Novel | POLD4 |
rs2668898 (11:61725498:G/A) | 0.402 | -5.83 | 5.32E-09 | 4 | 1 | Known | BEST1 |
rs180792704 (11:67325239:C:G) | 0.199 | -7.56 | 3.81E-14 | 5 | 1 | Novel | NA |
rs198434 (11:61483417:A:G) | 0.710 | -8.97 | 2.80E-19 | 6 | 1 | Known | DAGLA |
rs518804 (11:57494487:C:A) | 0.420 | -7.73 | 1.01E-14 | 7 | 1 | Novel | TMX2 |
rs3177514 (11:66130358:G:T) | 0.699 | -5.60 | 2.06E-08 | 8 | 1 | Novel | SLC29A2 |
ALA | rs174562 (11:61585144:G:A) | 0.503 | 7.84 | 4.30E-15 | 1 | 23 | Known | FADS1 |
DGLA | rs174538 (11:61560081:A:G) | 0.488 | 14.70 | 6.03E-49 | 1 | 1 | Known | TMEM258 |
rs174585 (11:61611694:A:G) | 0.274 | 9.82 | 8.72E-23 | 2 | 1 | Known | FADS2 |
rs198434 (11:61483417:A:G) | 0.710 | 6.27 | 3.57E-10 | 3 | 1 | Known | DAGLA |
rs198461 (11:61524366:C:A) | 0.363 | -5.95 | 2.54E-09 | 4 | 1 | Known | MYRF |
rs57112407 (15:78088914:T:C) | 0.255 | -5.86 | 4.46E-09 | NA | NA | Novel | LINGO1 |
rs4985155 (16:15129459:G:A) | 0.524 | -7.72 | 1.16E-14 | 1 | 25 | Known | PDXDC1 |
DPA | rs1535 (11:61597972:G:A) | 0.520 | -11.31 | 1.07E-29 | 1 | 18 | Known | FADS2 |
rs198434 (11:61483417:A:G) | 0.710 | -6.26 | 3.67E-10 | 2 | 1 | Known | DAGLA |
EPA | rs102274 (11: 61557826:C:T) | 0.506 | -11.56 | 6.18E-31 | 1 | 17 | Known | TMEM258 |
GLA | rs174576 (11: 61603510:A:C) | 0.546 | -7.73 | 1.07E-14 | 1 | 19 | Known | FADS2 |
LA | rs174564 (11:61588305:G:A) | 0.520 | 15.11 | 1.23E-51 | 1 | 10 | Known | FADS2 |
rs10751002 (11:63617634:G:T) | 0.664 | 6.06 | 1.36E-09 | 2 | 1 | Novel | MARK2 |
rs2668898 (11:61725498:G:A) | 0.402 | 5.54 | 2.99E-08 | 3 | 1 | Known | BEST1 |
rs28364240 (11:67120530:G:C) | 0.204 | 5.90 | 3.44E-09 | 4 | 1 | Novel | POLD4 |
rs11039018 (11:46909524:A:C) | 0.67 | -6.10 | 1.01E-09 | 5 | 1 | Novel | LRP4 |
rs518804 (11:57494487:C:A) | 0.420 | 6.03 | 1.62E-09 | 6 | 1 | Known | TMX2 |
Table 2 shows the signals (credible sets) of putative causal variants identified at each chromosome for each PUFAs from SuSiE in the HIS. All variant positions are presented based on Human Genome Build 37. Variants previously documented in the CHARGE GWAS meta-analysis of n-3 and n-6 PUFAs were considered known prior to the current meta-analysis. Additionally, those variants demonstrating linkage disequilibrium (LD) R-squared > 0.2 with one or more previously reported GWAS variants were considered known. The remaining variants that were not in LD with known GWAS variants were considered novel in the current study. There was only one genome-wide significant variant on chromosome 15 for DGLA (rs57112407) in HIS, this signal was not carried forward for fine-mapping.
Table 3
Genome-wide significant signals (Credible sets) for PUFAs in CHARGE African Americans.
| Variants (Chr:Pos:EFF:OTH) | EAF | Zscore | Pvalue | Cluster | # Of SNP | Novel/ Known | Nearest Gene |
AA | rs174585 (11:61611694:A:G) | 0.060 | -9.32 | 1.08E-20 | 1 | 1 | Known | FADS2 |
rs174607 (11:61627321:C:G) | 0.078 | -6.49 | 8.47E-11 | 2 | 1 | Known | FADS2 |
rs174564 (11:61588305:G:A) | 0.133 | -14.85 | 6.43E-50 | 3 | 1 | Known | FADS2 |
rs174559 (11:61581656:A:G) | 0.078 | -13.68 | 1.27E-42 | 4 | 1 | Known | FADS1 |
rs17161592 (7:9388418:C:G) | 0.085 | -6.31 | 2.75E-10 | 1 | 2 | Novel | NA |
DGLA | rs174560 (11:61581764:C:T) | 0.216 | 9.12 | 7.51E-20 | 1 | 1 | Known | FADS1 |
rs1136001 (16:15131974:T:G) | 0.220 | -6.11 | 9.69E-10 | 2 | 17 | Known | PDXDC1 |
DPA | rs717894 (6:22119292:A:G) | 0.250 | -5.48 | 4.11E-08 | 1 | 1 | Novel | CASC15 |
rs9295741 (6:10997166:T:C) | 0.223 | 5.54 | 2.89E-08 | 2 | 2 | Known | ELOVL2 |
DHA | rs114622288 (10:14663844:A:G) | 0.050 | -5.71 | 1.16e-08 | NA | NA | Novel | FAM107B |
LA | rs28456 (11:61597972:G:A) | 0.163 | 7.88 | 3.14E-15 | 1 | 2 | Known | FADS2 |
Table 3 shows the signals (credible sets) of putative causal variants identified at each chromosome for each PUFAs from SuSiE in AFA. All variant positions are presented based on Human Genome Build 37. Variants previously documented in the CHARGE GWAS meta-analysis of n-3 and n-6 PUFAs were considered known at the current meta-analysis. Additionally, those variants demonstrating linkage disequilibrium (LD) R-squared > 0.2 with one or more previously reported GWAS variants were considered known. The remaining variants that were not in LD with known GWAS variants were considered novel in the current study. There was only one genome-wide significant variant on chromosome 10 for DHA (rs114622288) in AFA, this signal was not carried forward for fine-mapping.
We identified multiple independent putative causal signals for the PUFA traits [AA: 8 signals (credible sets); ALA: 1; DGLA: 5, DPA: 2; EPA: 1; GLA: 1; LA: 6] in HIS and [AA: 5; DGLA: 2, DPA: 2, LA: 1] in AFA (Table 2, Table 3, Table S2 and Table S3). We examined the overlap of signals identified from fine-mapping in HIS versus AFA. We observed that the credible sets were generally smaller in AFA (average number of variants in credible set: HIS:3.4; AFR:2.2) possibly driven by the lower average LD in AFA.
Among the independent credible sets identified, most were novel associated signals within a +/- 5 Mb region of the previously reported FADS signal on chromosome 11 (Tables 2–3). Examining all the signals for PUFAs in HIS and AFA, we observed that the lead signal (reflecting the strongest evidence of association) on chromosome 11 represents the FADS signal reported in the previous GWAS.20 For example, rs174547, the FADS1 variant reported in the previous CHARGE EUR GWAS, is one of the variants in the first credible set for AA in HIS.19,20 In addition to the known FADS signals, we also observed multiple novel independent signals at other regions of chromosome 11 for PUFAs [AA: 5 novel signals (credible sets) and LA: 3] in HIS, for example, in/near ANKRD13D, TMX2, POLD4 and SLC29A2 and spanning a long range (57.5Mb ~ 67.1Mb) on chromosome 11 for AA in HIS (Table 2). Additionally, we observed several novel independent signals on other chromosomes showing associations with the PUFA traits in AFA [AA: 1 novel signal on chromosome 7 and DPA: 1 on chromosome 6] (Table 3).
Additional independent PUFA-associated signals on chromosome 11 demonstrate chromatin contacts with FADS and other genes
While prior studies have represented the FADS signal as primarily just one signal,19,20 our study demonstrates numerous independent signals within the FADS region (+/- 1Mb of the top variant, rs107724) (Fig. 2A). We examined this region to identify the subset of variants that may affect cis-regulatory elements in physical contact with nearby genes. Four variants within the credible sets in this region were located in regions of open chromatin defined by ATAC-seq and were in contact with gene promoters defined by Promoter Capture C in multiple metabolic-relevant cell types (human mesenchymal stem cells [hMSC], adipocytes derived from in vitro from the hMSC [hMSC_Adipocytes], induced pluripotent stem cell derived Hepatocytes [iPSC_Hepatocytes], embryonic stem cell derived Hypothalamic Neurons [hESC_HypothalamicNeurons], Enteroids, and HepG2s). Almost all of the interactions we detected were bait-to-bait interactions, meaning that they reflected physical contact between promoters of two different genes (Table S4). For example, the region surrounding rs2668898 near BEST1 showed evidence of physical contact with the TMEM258, FADS1 and FADS2 region in multiple cell types and TMEM258 region also showed evidence of physical contact with the FADS1 and FADS2 region (Fig. 3A and Table S4). Besides the FADS region, we further found evidence of physical contact between POLD4 and ANKRD13D(Fig. 3B and Table S4), corresponding to the regions surrounding two signals identified in fine-mapping of AA in HIS (Fig. 2A).
Three novel signals on chromosome 11 identified in HIS show evidence of cross-ancestry replication or validation
We examined evidence of cross-ancestry replication for signals identified in our present GWAS of CHARGE HIS and AFA by examining evidence of genetic association in European Americans (CHARGE EUR and MESA EUR), African Americans (CHARGE AFA), Hispanic Americans (CHARGE HIS) and Chinese Americans (MESA CHN). Replication analysis was performed with multiple testing correction (HIS: P < 0.05/19 signals = 0.0026 and AFA: P < 0.05/11 signals = 0.004).
As noted previously, the first credible set identified in our present GWAS of HIS and AFA for each trait (reflecting the strongest evidence of association) generally coincided with the region of chromosome 11 reported in prior CHARGE GWAS efforts. These signals showed evidence of genetic association in European Americans, as well as across race/ancestry groups. For example, rs102274 for AA was replicated in the MESA EUR, CHARGE AFA and MESA CHN groups (MESA EUR: P = 1.04 x 10− 151, CHARGE AFA: P = 2.36 x 10− 47, MESA CHN: P = 8.75 x 10− 92) (Table S5).
Additionally, one novel signal was also replicated across race/ancestry groups (Table 4). LRP4 variant rs11039018 in credible set 5 for LA was replicated in the CHARGE AFA (CHARGE AFA: P = 1.90 x 10− 13).
Table 4
Novel PUFA-associated signals (credible sets) from analysis of HIS with external replication or validation evidence.
Traits | Variants (chr:pos:effect:other) | Replication | Validation | Direction | Nearest Gene |
AA | rs518804 (11:57494487:C:A) | NS | HDL: P = 1.96E-06 logTG: P = 0.001 | HDL: (-) LDL: (-) logTG: (+) | TMX2 |
LA | rs10751002 (11:63617634:G:T) | NS | LDL: P = 3.31E-12 TC: P = 5.74E-09 | LDL: (+) TC: (+) | MARK2 |
rs11039018 (11:46909524:A:C) | AFA: P = 1.90E-13 | HDL: P = 2.85E-74 logTG: P = 4.5E-43 | AFA: (+) HDL: (+) logTG: (-) | LRP4 |
Table 4 shows the novel putative causal variants in each signal (credible set) identified from Fine-mapping for PUFAs with replication and validation evidence in HIS. Variants that weren’t previously documented in the CHARGE GWAS meta-analysis of n-3 and n-6 PUFAs and weren’t in LD with known GWAS variants were considered novel in the current study.
Some of the novel signals without cross-ancestry replication demonstrated large differences in allele frequencies across groups. For example, the effect allele frequency of rs28364240, a POLD4 missense variant in credible set 3 for AA in Hispanics, is 0.204 in our CHARGE HIS group, but close to zero in the other race/ancestry groups examined (EUR: 0.003, AFR: 0.007, CHN: 0.005) (Fig. 2B and Table S5) and the effect allele frequency of rs142068305, a ANKRD13D intron variant, is 0.196 in our CHARGE HIS group while 0.007, 0.004 and 0.005 in AFR, EUR and CHN, respectively. These results suggest evidence of genetic association signals unique to HIS or other groups carrying Amerindian ancestry or admixture.
As some variants could not be interrogated using independent GWAS of PUFA traits, given those studies’ focus on specific race/ancestry groups which may not include our variants of interest and/or limited sample sizes, we performed validation analyses using the results of multi-ancestry GWAS of lipid levels from the GLGC including ~ 1.65 million individuals from five genetic ancestry groups (admixed African or African, East Asian, European, Hispanic and South Asian). We focused on the most significant putative causal variants from each credible set and applied multiple testing correction for the number of validated variants (HIS: P < 0.05/19 = 0.0026 and AFA: P < 0.05/11 = 0.004). Interestingly, we observed that two novel signals without cross-ancestry replication did demonstrate association with one or more lipid levels. For example, the AA associated TMX2 intron variant rs518804 was validated based on its association with HDL and Triglycerides (HDL: 1.96 x 10− 06 and Triglycerides: 0.001), while the LA associated MARK2 intron variant rs10751002 was validated based on its association with LDL and Total Cholesterol (LDL: 3.31 x 10− 12 and Total Cholesterol: 5.74 x 10− 09) (Table 4, Table S7 and Table S8).
Integrative Analyses Identify Putative Causal Genes For The Pufa Loci
Using colocalization with eQTL resources, we identified candidate genes underlying the genetic association signals for the PUFA traits. In HIS, we found colocalization with expression of the genes MED19, TMEM258, PACS1, RAD9A, C11orf24, CTTN on chromosome 11 and PDXDC1 on chromosome 16 based on MESA multi-ancestry eQTL resources26 (Table 5and Table S9). In further analysis using eQTL resources from GTEx whole blood, we confirmed colocalization with TMEM258 and MED19 identified using the MESA multi-ancestry eQTLs, and also identified colocalization with FADS1, RPS4XP13, AP001462.2, PGA5, PGA5, TPCN2, MEN1 on chromosome 11 and RP11-156C22.5 on chromosome 16. (Table 5and Table S10).
Table 5
Integrative analysis (Colocalization and PrediXcan) in the Hispanic Americans using multi-ancestry resources from MESA and GTEx.
| Colocalization Analysis | PrediXcan |
| MESA multi-ethnics eQTLs | GTEx eQTLs | MESA | GTEx |
AA | Chromosome 11 |
MED19, TMEM258, PACS1, RAD9A | RPS4XP13, AP001462.6 | TMEM258, TMEM109, ZBTB3, TTC9C, FERMT3, MED19, POLD4, CLCF1, INCENP, MADD, SSH3, C11orf24, PRPF19, TBC1D10C, BANF1, CCDC86, NXF1, MS4A6E, CCS, COX8A, CCDC88B, ACP2, MAP4K2 | TMEM258, TMEM223, NXF1, INCENP, MUS81, C11orf84, MED19, MEN1, BBS1, NEAT1, DPP3, SSH3, ACP2, ASRGL1, RNASEH2C |
ALA | Chromosome 11 |
TMEM258, MED19 | MED19, PGA5, TMEM258 | TMEM258, TMEM109 | TMEM258 |
DGLA | Chromosome 11 |
TMEM258 | | TMEM258, ZBTB3 | TMEM258, FADS1, FADS2 |
Chromosome 16 |
PDXDC1 | RP11-426C22.5 | PDXDC1 | NPIPA2 |
DPA | Chromosome 11 |
TMEM258, C11orf24, RAD9A | PGA5 | TMEM258, TMEM109 | TMEM258, SSH3, TMEM223 |
EPA | Chromosome 11 |
TMEM258 | TPCN2 | TMEM258, FERMT3, TMEM109 | TMEM258, SSH3, TMEM223 |
GLA | Chromosome 11 |
TMEM258 | MEN1 | TMEM258 | TMEM258 |
| Chromosome 11 |
LA | MED19, CTTN, C11orf24, RAD9A | MED19, TPCN2, FADS1, RPS4XP13, AP001462.6 | TMEM258, TMEM109, FERMT3, ZBTB3, COX8A, MADD, POLD4, TBC1D10C, INCENP, TTC9C, MED19, CLCF1, SSH3, ACP2 | TMEM258, INCENP, SSH3, C11orf84, TMEM223, GIF, NXF1, MED19, MUS81, ACP2 |
Table 5 shows the results of integrative analysis including Colocalization analysis and PrediXcan in the HIS by using MESA data and GTEx data. For Colocalization analysis, eQTL resources include MESA multi-ethnic eQTL from purified monocytes and GTEx European ancestry whole blood tissue eQTL. GWAS signals with posterior colocalization probability of hypothesis 4 (PP.H4) > 0.80, or PP.H4 > 0.50 and the ratio of PP.H4 / PP.H3 > 5 were considered colocalized with eQTL. For PrediXcan, reference gene expression prediction models include MESA purified monocytes and GTEx European ancestry whole blood. Multiple testing correction of PrediXcan was applied for all genes (MESA: P < 0.05/4470 = 0.00001 and GTEx: P < 0.05/4350 = 0.00001).
We also performed complementary integrative analysis using PrediXcan, identifying significant associations for predicted expression of TMEM258 with AA, ALA, DGLA, DPA, EPA, GLA and LA (after multiple testing correction for all genes examined: P < 0.05/4470 = 0.00001), based on integration with eQTL from both MESA and GTEx. PrediXcan also identified TMEM109, ZBTB3, TTC9C, POLD4, INCENP and FERMT3 on chromosome 11 and PDXDC1 on chromosome 16 as putative genes associated with PUFAs in HIS (Table 5, Table S11 and Table S12). For AFA, colocalization and PrediXcan analyses did not identify any genes of interest that met our pre-specified thresholds for statistical significance.
Incorporating the prior chromatin contacts identified (Table S4), we found that several of our GWAS regions had physical contact with one or more genes identified by integration with eQTL resources. For example, RAD9A was supported by colocalization with MESA eQTL and also showed chromatin contact with POLD4 in nearly all cell types examined (Fig. 3B). In addition, INCENP was supported by PrediXcan using both MESA and GTEx resources and also showed chromatin contact with TMEM258, FADS1 and FADS2 in nearly all cell types examined (Fig. 3A). We further observed that CLCF1, RAD9A, FADS2, TMEM258, INCENP, FADS1 identified from colocalization or PrediXcan were additionally supported by chromatin contacts analyses (Table S4, Fig. 3A and 3B).
To follow-up on the genes of interest identified by colocalization and PrediXcan analyses, we examined their co-expression with FADS1 using GTEx whole blood gene expression with multiple testing correction for the number of genes under consideration (HIS: P < 0.05/39 = 0.0012). In both unadjusted and age/sex-a djusted regression models, multiple genes showed statistically significant co-expression with FADS1, for example, TMEM258, MED19, POLD4, RAD9A and SSH3 (Table S13), suggesting these genes have shared patterns of expression.