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Table 1 Nuclear-encoded genetic variation significantly associated with inferred mitochondrial RNA cleavage rates in discovery (CARTaGENE) data and statistics for the same associations in replication (GTEx) data. Variants are linked to genes either through functional (missense) mutations or via eQTL data

From: Identification of human mitochondrial RNA cleavage sites and candidate RNA processing factors

Cleavage Site Peak nuclear SNP Chr Position Annotation eQTL Nearest nuclear gene CaG beta CaG P-value GTEx beta GTEx P-value
598 rs707009 3 66372144 Intron/NMD LIPA, LRIG1, SIRT1, SLC25A26 SLC25A26 0.012 9.8E−16 −0.011 2.8E−02
598 rs11156878 14 35735967 Missense NA MRPP3 −0.013 9.4E−11 −0.011 1.2E−01
3246 rs74422990 14 35726093 Intron MRPP3, PPP2R3C MRPP3 −0.036 4.3E−28 −0.028 3.7E−04
3258 rs11156878 14 35735967 Missense NA MRPP3 −0.010 4.3E−18 −0.004 1.5E−01
4252 rs74422990 14 35726093 Intron MRPP3, PPP2R3C MRPP3 −0.034 1.9E−14 −0.032 4.3E−05
4261 rs11156878 14 35735967 Missense NA MRPP3 −0.033 2.9E−19 −0.045 5.4E−04
4411 rs74422990 14 35726093 Intron MRPP3, PPP2R3C MRPP3 −0.064 1.0E−35 −0.078 2.5E−09
4438 rs11156878 14 35735967 Missense NA MRPP3 −0.013 1.2E−17 −0.002 6.6E−01
5511 rs11156878 14 35735967 Missense NA MRPP3 −0.037 3.2E−11 −0.014 2.4E−01
5911 rs35681402 20 3138626 Intron ITPA, UBOX5, PROSAPIP1, FASTKD5 UBOX5/FASTKD5 −0.050 3.5E−60 −0.058 5.1E−07
7514 rs74422990 14 35726093 Intron MRPP3, PPP2R3C MRPP3 −0.041 7.9E−13 −0.015 3.3E−01
7543 rs7158706 14 35736692 Intron MRPP3 MRPP3 −0.022 2.2E−17 −0.033 2.0E−03
8321 rs74422990 14 35726093 Intron MRPP3, PPP2R3C MRPP3 −0.019 5.4E−18 −0.005 5.3E−01
9194 rs75286457 20 3138134 Intron ITPA, UBOX5, PROSAPIP1, FASTKD5 UBOX5/FASTKD5 −0.016 8.6E−23 −0.014 1.7E−02
9205 rs75286457 20 3138134 Intron ITPA, UBOX5, PROSAPIP1, FASTKD5 UBOX5/FASTKD5 −0.031 8.0E−17 −0.043 1.7E−03
9219 rs35681402 20 3138626 Intron ITPA, UBOX5, PROSAPIP1, FASTKD5 UBOX5/FASTKD5 −0.040 6.9E−30 −0.042 1.6E−04
9219 rs113933961 7 45051924 Intron CCM2, RP4-647J21.1, MYO1G, SNHG15, NACAD, TBRG4, H2AFV CCM2/TBRG4 −0.023 6.5E−10 0.012 1.7E−01
9990 rs11156878 14 35735967 Missense NA MRPP3 −0.037 4.2E−11 −0.015 1.4E−01
10404 rs11156878 14 35735967 Missense NA MRPP3 −0.039 8.1E−11 −0.030 4.1E−03
10432 rs11156878 14 35735967 Missense NA MRPP3 −0.039 1.2E−24 −0.006 5.4E−01
12137 rs11156878 14 35735967 Missense NA MRPP3 −0.033 5.0E−11 −0.020 2.4E−02
12280 rs11156878 14 35735967 Missense NA MRPP3 −0.019 2.5E−16 −0.015 6.2E−02
14698 rs113933961 7 45051924 Intron CCM2, RP4-647J21.1, MYO1G, SNHG15, NACAD, TBRG4, H2AFV CCM2/TBRG4 −0.009 5.8E−10 0.001 7.3E−01
14716 rs73109897 7 45156242 Upstream gene CCM2, RP4-647J21.1, MYO1G, SNHG15, NACAD, TBRG4, H2AFV TBRG4 −0.013 8.9E−14 −0.007 6.5E−02
14758 rs4724362 7 45161303 Intergenic CCM2, RP4-647J21.1, MYO1G, SNHG15, NACAD, TBRG4, H2AFV TBRG4 −0.069 1.7E−10 −0.013 2.7E−01
15968 rs61988271 14 35741554 Intron MRPP3, SNX6 MRPP3 −0.024 3.6E−10 −0.026 3.5E−02