Table 2 Gene expression results for significant SNPs in GTEx and STARNET tissues

From: GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes

SNP

eQTLa (Gene, p) GTEx

eQTLa (Gene, p) STARNET tissues

AORb

HEART (ATR/VEN)c

AOR

MAM

rs201648240

CAMK1G, 0.0094

AL031316.1, 0.0040

  

CD34,0.00532

TRAF3IP3, 0.0097

rs6907215

 

AL023584.1, 0.005384704 (VEN)

ENSG00000217648, 0.00046

ENSG00000217648, 0.8 × 10−5

rs13225723

AC005050.1, 1 × 10−10

ENSG00000177820.5, 7.0 × 10−5

CCDC71L, 5 × 10−6

PRKAR2B, 4 × 10−8

PIK3CG, 10 × 10−3

 

CCDC71L, 6 × 10−36

PRKAR2B, 7 × 10−7

SYPL1, 0.0043

CCDC71L, 3 × 10−33

PRKAR2B, 6 × 10−8

NAMPT, 6 × 10−6

rs2912063

MCPH1, 0.0041

ENSG00000271743.1, 0.0093 (VEN)

MCPH1-AS1, 0.0020

 

rs11785239

 

AC022784.1, 0.0078 (VEN)

ERI1, 0.0069

PPP1R3B, 0.0036

rs844396

ENSG00000141012.8, 0.003

AC092384.2, 0.001

CBFA2T3, 1 × 10−7

ZNF469, 0.004 (ATR)

AC092384.3, 5 × 10−6 (ATR)

AC092384.1, 0.002 (ATR)

CBFA2T3, 0.0004 (ATR)

ZNF469, 0.002 (VEN)

AC138028.4, 0.001 (VEN)

ENSG00000224888.3, 0.009(VEN)

PIEZO1, 0.0004 (VEN)

GALNS, 0.004 (VEN)

RPL13, 0.0024

ZNF276, 0.0070

TRAPPC2L, 0.0091

TRAPPC2L, 0.0040

ZNF276, 0.0059

rs200495339

 

ENSG00000267105.1, 0.0005 (VEN)

  

rs148147734

DERL1, 0.0082

   

rs200482500

AF131215.6, 0.005

AF131215.5, 0.001

AF131215.5, 0.002 (ATR)

AF131215.6, 0.003 (VEN)

AF131215.5, 0.004 (VEN)

  

rs7412

ENSG00000267163.1, 0.007

   

rs11413744

PRMT9, 0.004

   

rs17477177

ENSG00000267052.1, 6 × 10−11

ENSG00000177820.5, 5 × 10−6

CCDC71L, 4 × 10−7

PRKAR2B, 2 × 10−8

BCAP29, 0.002 (ATR)

CCDC71L, 2 × 10−37

PRKAR2B, 6 × 10−7

SYPL1, 0.0091

CCDC71L,1 × 10−33

PRKAR2B, 2 × 10−8

NAMPT, 1 × 10−5

rs9632884

 

DMRTA1, 0.007 (ATR)

CDKN2B, 2 × 10−3

CDKN2B, 2 × 10−3

rs113309773

BCAR1, 6 × 10−11

ENSG00000261783.1, 2 × 10−16

GABARAPL2, 0.004

ENSG00000261783.1, 1 × 10−5 (ATR)

ENSG00000166822.8, 0.005 (ATR)

ENSG00000261783.1, 0.0003 (VEN)

ZFP1, 4 × 10−4

AC009078.2, 0.002

BCAR1, 3 × 10−12

CFDP1, 0.002

TMEM170A, 0.009

 
  1. p = p-values of association from linear regression analysis
  2. aThe lead SNP from GWAS is considered an eQTL if the cis-association has a nominal p-value of association <0.01. Multiple but not all lead SNPs reach genome-wide significance (p < 10−4).
  3. bThis includes aorta (AOR)
  4. cThis includes heart atrial (ATR) and heart left ventricle (VEN)
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