Variant report

Variant	rs316614
Chromosome Location	chr15:41746625-41746626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10152497	0.86[ASN][1000 genomes]
rs10153010	0.86[ASN][1000 genomes]
rs10467974	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs10518718	0.93[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11630191	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631770	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11633799	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs12324291	0.83[ASN][1000 genomes]
rs13379756	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap]
rs1655556	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1655557	0.80[EUR][1000 genomes]
rs16971767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs16971798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16971806	0.93[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs16971832	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16971834	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1757455	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1757456	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs1757463	0.87[CHB][hapmap];0.84[LWK][hapmap]
rs2015781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2777491	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28393472	0.86[ASN][1000 genomes]
rs28526381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs28557159	0.88[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs28578057	0.83[ASN][1000 genomes]
rs28583065	0.83[ASN][1000 genomes]
rs28600680	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28655070	0.93[ASN][1000 genomes]
rs28716108	0.86[ASN][1000 genomes]
rs28792672	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28847691	0.96[ASN][1000 genomes]
rs316605	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316610	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316613	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316615	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs316617	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap]
rs35826725	0.93[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs3743038	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55782852	0.83[ASN][1000 genomes]
rs59590312	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61037359	0.82[ASN][1000 genomes]
rs6650519	0.81[ASN][1000 genomes]
rs66538814	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66591771	0.83[EUR][1000 genomes]
rs7161772	0.83[ASN][1000 genomes]
rs7163649	0.82[ASN][1000 genomes]
rs7163788	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7165675	0.83[ASN][1000 genomes]
rs7167498	0.93[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs7167729	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7168177	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7168307	0.83[ASW][hapmap];0.80[GIH][hapmap]
rs7172148	0.92[ASN][1000 genomes]
rs7175800	0.93[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7176588	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs7177641	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7178634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7178777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7180418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7180492	0.91[ASN][1000 genomes]
rs7181911	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7182667	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7182700	0.92[EUR][1000 genomes]
rs73404987	0.81[ASN][1000 genomes]
rs73404994	0.86[ASN][1000 genomes]
rs73404995	0.86[ASN][1000 genomes]
rs73404996	0.86[ASN][1000 genomes]
rs73405000	0.83[ASN][1000 genomes]
rs73405001	0.83[ASN][1000 genomes]
rs73407109	0.86[ASN][1000 genomes]
rs8023530	0.83[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs8024774	0.84[CEU][hapmap];0.80[CHB][hapmap];0.85[TSI][hapmap]
rs8026197	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8027626	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8032838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs8034626	0.81[ASN][1000 genomes]
rs8034819	0.89[ASN][1000 genomes]
rs8036498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs8036527	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8037574	0.83[ASW][hapmap];0.81[GIH][hapmap]
rs8037824	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8041325	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs823716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9302109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs9672866	0.82[ASN][1000 genomes]
rs9972288	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
3	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs316614	NDUFAF1	cis	multi-tissue	Pritchard
rs316614	NDUFAF1	cis	cerebellum	SCAN
rs316614	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs316614	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs316614	STARD9	cis	cerebellum	SCAN
rs316614	RPAP1	cis	parietal	SCAN
rs316614	NDUFAF1	cis	Muscle Skeletal	GTEx
rs316614	NUSAP1	cis	cerebellum	SCAN
rs316614	NDUFAF1	cis	parietal	SCAN
rs316614	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs316614	ZFP106	cis	parietal	SCAN
rs316614	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs316614	OIP5-AS1	cis	Artery Tibial	GTEx
rs316614	NUSAP1	cis	parietal	SCAN
rs316614	NDUFAF1	cis	Thyroid	GTEx
rs316614	OIP5-AS1	cis	Nerve Tibial	GTEx
rs316614	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs316614	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs316614	NDUFAF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41710400-41750000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41711600-41746800	Weak transcription	A549	lung
3	chr15:41711600-41759000	Weak transcription	Fetal Heart	heart
4	chr15:41719000-41749800	Weak transcription	NHLF	lung
5	chr15:41719000-41765800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:41722000-41749200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:41722000-41749600	Weak transcription	Gastric	stomach
8	chr15:41722000-41768400	Weak transcription	Small Intestine	intestine
9	chr15:41724200-41777200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:41728200-41749800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:41729200-41773000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:41729400-41756200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:41730000-41768400	Weak transcription	Psoas Muscle	Psoas
14	chr15:41730400-41749800	Weak transcription	Brain Substantia Nigra	brain
15	chr15:41730600-41746800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr15:41730800-41769000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:41732400-41747200	Weak transcription	Aorta	Aorta
18	chr15:41732800-41749800	Weak transcription	Colonic Mucosa	Colon
19	chr15:41734000-41747400	Weak transcription	NHEK	skin
20	chr15:41734000-41750200	Weak transcription	Fetal Brain Male	brain
21	chr15:41734200-41749600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:41734200-41749600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr15:41734200-41749800	Weak transcription	Right Ventricle	heart
24	chr15:41734200-41749800	Weak transcription	K562	blood
25	chr15:41734200-41750400	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:41734200-41758800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr15:41734800-41749800	Weak transcription	HUVEC	blood vessel
28	chr15:41735000-41749800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:41735400-41749800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:41735600-41749800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:41735800-41746800	Weak transcription	Fetal Lung	lung
32	chr15:41735800-41746800	Weak transcription	HepG2	liver
33	chr15:41735800-41749800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr15:41735800-41749800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr15:41735800-41749800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:41735800-41749800	Weak transcription	Fetal Kidney	kidney
37	chr15:41735800-41749800	Weak transcription	NH-A	brain
38	chr15:41735800-41750200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:41739800-41749800	Weak transcription	NHDF-Ad	bronchial
40	chr15:41740000-41746800	Weak transcription	GM12878-XiMat	blood
41	chr15:41743200-41751600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:41743600-41748400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr15:41743800-41748600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:41743800-41750000	Strong transcription	Placenta	Placenta
45	chr15:41743800-41751000	Strong transcription	Primary T cells from cord blood	blood
46	chr15:41743800-41751600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:41743800-41751600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr15:41743800-41751600	Strong transcription	Fetal Muscle Leg	muscle
49	chr15:41743800-41751800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:41743800-41752000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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