Variant report

Variant	rs316611
Chromosome Location	chr15:41751678-41751679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10518717	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11070328	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs11629979	1.00[ASN][1000 genomes]
rs11630656	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs11630799	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11635906	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854081	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11854632	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs16971726	1.00[CHB][hapmap]
rs170296	1.00[LWK][hapmap]
rs1757457	1.00[LWK][hapmap]
rs1757468	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730589	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs17730888	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2730056	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28374715	1.00[CHB][hapmap]
rs28377562	1.00[ASN][1000 genomes]
rs28416360	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28421136	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	1.00[ASN][1000 genomes]
rs28456082	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458941	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28459164	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28463309	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs28477406	1.00[ASN][1000 genomes]
rs28492932	1.00[ASN][1000 genomes]
rs28493702	1.00[CHB][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs28535540	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28555198	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs28576457	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584379	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	1.00[ASN][1000 genomes]
rs28631111	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs28661013	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663426	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673484	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	1.00[ASN][1000 genomes]
rs28700583	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703570	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	1.00[ASN][1000 genomes]
rs28897479	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316604	0.86[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316606	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316607	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316616	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204853	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34040639	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34285452	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34665396	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924549	1.00[CHB][hapmap]
rs55725658	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56400990	1.00[ASN][1000 genomes]
rs59000092	1.00[ASN][1000 genomes]
rs6493000	1.00[ASN][1000 genomes]
rs6493003	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162231	1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7164211	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164684	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	1.00[ASN][1000 genomes]
rs7165914	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs7168431	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];1.00[ASN][1000 genomes]
rs7181982	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7182324	1.00[ASN][1000 genomes]
rs72739630	1.00[ASN][1000 genomes]
rs72739644	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs8034840	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8036734	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs8038132	1.00[ASN][1000 genomes]
rs8041809	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568	1.00[CHB][hapmap];1.00[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs316611	NDUFAF1	cis	multi-tissue	Pritchard
rs316611	NDUFAF1	cis	Whole Blood	GTEx
rs316611	OIP5-AS1	cis	Artery Tibial	GTEx
rs316611	KRTAP4-7	cis	normal skin	skin_eQTL
rs316611	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs316611	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs316611	NDUFAF1	cis	Thyroid	GTEx
rs316611	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs316611	NDUFAF1	cis	lung	GTEx
rs316611	NDUFAF1	cis	Muscle Skeletal	GTEx
rs316611	OIP5-AS1	cis	Nerve Tibial	GTEx
rs316611	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs316611	KRTAP4-7	cis	lesional skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41711600-41759000	Weak transcription	Fetal Heart	heart
2	chr15:41719000-41765800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:41722000-41768400	Weak transcription	Small Intestine	intestine
4	chr15:41724200-41777200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:41729200-41773000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:41729400-41756200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:41730000-41768400	Weak transcription	Psoas Muscle	Psoas
8	chr15:41730800-41769000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:41734200-41758800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:41743800-41751800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr15:41743800-41752000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:41743800-41762200	Weak transcription	Stomach Mucosa	stomach
13	chr15:41744000-41771800	Strong transcription	Fetal Intestine Small	intestine
14	chr15:41744200-41767400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:41744600-41752400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr15:41744600-41752800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:41745000-41751800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:41745000-41752000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr15:41745200-41752200	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr15:41745200-41752800	Strong transcription	Brain Germinal Matrix	brain
21	chr15:41745200-41766800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:41745200-41775800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:41745800-41754400	Weak transcription	Brain Angular Gyrus	brain
24	chr15:41745800-41763400	Weak transcription	Pancreas	Pancrea
25	chr15:41748000-41761000	Weak transcription	A549	lung
26	chr15:41748600-41756000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:41749200-41753000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:41749400-41752200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:41749400-41752400	Strong transcription	GM12878-XiMat	blood
30	chr15:41749400-41753000	Strong transcription	Liver	Liver
31	chr15:41749600-41752800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:41749600-41756000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:41749800-41751800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:41749800-41751800	Strong transcription	NHDF-Ad	bronchial
35	chr15:41749800-41752000	Strong transcription	Osteobl	bone
36	chr15:41749800-41752200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:41749800-41752200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr15:41749800-41752400	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr15:41749800-41752800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr15:41749800-41752800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:41749800-41752800	Strong transcription	Dnd41	blood
42	chr15:41749800-41753000	Strong transcription	Duodenum Mucosa	Duodenum
43	chr15:41749800-41753000	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:41749800-41756000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:41750000-41751800	Strong transcription	Hela-S3	cervix
46	chr15:41750600-41752800	Strong transcription	Placenta	Placenta
47	chr15:41750600-41754600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr15:41750600-41757400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr15:41750600-41757600	Weak transcription	NHEK	skin
50	chr15:41750600-41761200	Weak transcription	Right Ventricle	heart

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