Table 2.
Open in new tab

Expression quantitative trait loci (eQTL) for pathway single-nucleotide polymorphisms (SNPs) in normal pancreatic tissue from GTEx and an independent replication set

Pathway geneChrr2 with rs876493*SNPeQTL geneGTEx pancreas (n = 220)
Independent LTG pancreas (n = 95)
P†Effect size (β)‡P†Effect size (β)‡
ERBB2, PGAP317N/Ars876493 §,‖PGAP33.90 × 10−7−0.241.16 × 10−5−.43
TCAP, STARD3, PNMT17.636rs3764351 §,‖PGAP35.70 × 10−9−.309.70 × 10−5−.47
GRB7, MIEN117.3508rs4795393§PGAP34.00 × 10−10−.303.83 × 10−5−.45
GSDMB, ZPBP217.3046rs12453507§PGAP32.70 × 10−7−.222.80 × 10−5−.45
CASP710–rs3124737‖CASP72.50 × 10−8.42.02.28
Pathway geneChrr2 with rs876493*SNPeQTL geneGTEx pancreas (n = 220)
Independent LTG pancreas (n = 95)
P†Effect size (β)‡P†Effect size (β)‡
ERBB2, PGAP317N/Ars876493 §,‖PGAP33.90 × 10−7−0.241.16 × 10−5−.43
TCAP, STARD3, PNMT17.636rs3764351 §,‖PGAP35.70 × 10−9−.309.70 × 10−5−.47
GRB7, MIEN117.3508rs4795393§PGAP34.00 × 10−10−.303.83 × 10−5−.45
GSDMB, ZPBP217.3046rs12453507§PGAP32.70 × 10−7−.222.80 × 10−5−.45
CASP710–rs3124737‖CASP72.50 × 10−8.42.02.28
*

Linkage disequilibrium r2 values are derived from LDLink EUR population data. Chr = chromosome; eQTL = expression quantitative trait loci; FDR = false discovery rate; LTG = Laboratory of Translational Genomics; TSS = transcription start site.

†

eQTL in pancreas FDR (≤ 0.05) using roughly 1 Mb cis-window around TSS. Statistical test was two-sided.

‡

Beta (β) eQTL directional effect for risk allele.

§

SNP in the Nikolsky breast cancer chr17 amplicon gene set.

‖

SNP in the Pujana ATM PCC network gene set.

Table 2.
Open in new tab

Expression quantitative trait loci (eQTL) for pathway single-nucleotide polymorphisms (SNPs) in normal pancreatic tissue from GTEx and an independent replication set

Pathway geneChrr2 with rs876493*SNPeQTL geneGTEx pancreas (n = 220)
Independent LTG pancreas (n = 95)
P†Effect size (β)‡P†Effect size (β)‡
ERBB2, PGAP317N/Ars876493 §,‖PGAP33.90 × 10−7−0.241.16 × 10−5−.43
TCAP, STARD3, PNMT17.636rs3764351 §,‖PGAP35.70 × 10−9−.309.70 × 10−5−.47
GRB7, MIEN117.3508rs4795393§PGAP34.00 × 10−10−.303.83 × 10−5−.45
GSDMB, ZPBP217.3046rs12453507§PGAP32.70 × 10−7−.222.80 × 10−5−.45
CASP710–rs3124737‖CASP72.50 × 10−8.42.02.28
Pathway geneChrr2 with rs876493*SNPeQTL geneGTEx pancreas (n = 220)
Independent LTG pancreas (n = 95)
P†Effect size (β)‡P†Effect size (β)‡
ERBB2, PGAP317N/Ars876493 §,‖PGAP33.90 × 10−7−0.241.16 × 10−5−.43
TCAP, STARD3, PNMT17.636rs3764351 §,‖PGAP35.70 × 10−9−.309.70 × 10−5−.47
GRB7, MIEN117.3508rs4795393§PGAP34.00 × 10−10−.303.83 × 10−5−.45
GSDMB, ZPBP217.3046rs12453507§PGAP32.70 × 10−7−.222.80 × 10−5−.45
CASP710–rs3124737‖CASP72.50 × 10−8.42.02.28
*

Linkage disequilibrium r2 values are derived from LDLink EUR population data. Chr = chromosome; eQTL = expression quantitative trait loci; FDR = false discovery rate; LTG = Laboratory of Translational Genomics; TSS = transcription start site.

†

eQTL in pancreas FDR (≤ 0.05) using roughly 1 Mb cis-window around TSS. Statistical test was two-sided.

‡

Beta (β) eQTL directional effect for risk allele.

§

SNP in the Nikolsky breast cancer chr17 amplicon gene set.

‖

SNP in the Pujana ATM PCC network gene set.

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