Variant report

Variant	rs316610
Chromosome Location	chr15:41752852-41752853
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10152497	0.82[ASN][1000 genomes]
rs10153010	0.82[ASN][1000 genomes]
rs10467974	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs10518718	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs11630191	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11631770	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11633799	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs13379756	0.95[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap]
rs1622914	0.82[EUR][1000 genomes]
rs1655556	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1655557	0.85[EUR][1000 genomes]
rs16971767	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs16971798	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16971806	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs16971832	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16971834	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1757455	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1757456	0.84[CEU][hapmap]
rs1757463	0.81[CHB][hapmap];0.87[LWK][hapmap]
rs2015781	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2777491	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28393472	0.82[ASN][1000 genomes]
rs28526381	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs28557159	0.94[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs28600680	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28655070	0.89[ASN][1000 genomes]
rs28716108	0.82[ASN][1000 genomes]
rs28792672	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28847691	0.92[ASN][1000 genomes]
rs316605	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316609	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316613	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs316614	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]
rs316615	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs316617	0.81[CEU][hapmap];0.81[CHB][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs35826725	0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs3743038	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59590312	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66538814	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66591771	0.81[EUR][1000 genomes]
rs7163788	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7167498	0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs7167729	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7168177	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7168307	0.88[ASW][hapmap];0.80[GIH][hapmap]
rs7172148	0.88[ASN][1000 genomes]
rs7175800	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7176588	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7177641	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7178634	1.00[CEU][hapmap];0.93[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];0.93[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];0.93[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7180492	0.92[ASN][1000 genomes]
rs7181911	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7182667	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7182700	0.90[EUR][1000 genomes]
rs73404994	0.82[ASN][1000 genomes]
rs73404995	0.82[ASN][1000 genomes]
rs73404996	0.82[ASN][1000 genomes]
rs73407109	0.82[ASN][1000 genomes]
rs8023530	0.89[ASW][hapmap];0.81[GIH][hapmap];0.82[YRI][hapmap]
rs8024774	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs8026197	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8027626	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8032838	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs8034819	0.86[ASN][1000 genomes]
rs8036498	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs8036527	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037574	0.89[ASW][hapmap];0.81[GIH][hapmap]
rs8037824	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8041325	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs919961	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9302109	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs9972288	0.87[EUR][1000 genomes];0.83[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
rs316610	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs316610	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs316610	OIP5-AS1	cis	Artery Tibial	GTEx
rs316610	NDUFAF1	cis	cerebellum	SCAN
rs316610	NDUFAF1	cis	Thyroid	GTEx
rs316610	NUSAP1	cis	parietal	SCAN
rs316610	NUSAP1	cis	cerebellum	SCAN
rs316610	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs316610	NDUFAF1	cis	parietal	SCAN
rs316610	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs316610	NDUFAF1	cis	lymphoblastoid	seeQTL
rs316610	NDUFAF1	cis	Muscle Skeletal	GTEx
rs316610	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs316610	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs316610	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs316610	RPAP1	cis	parietal	SCAN
rs316610	NDUFAF1	cis	multi-tissue	Pritchard
rs316610	STARD9	cis	cerebellum	SCAN
rs316610	OIP5-AS1	cis	Nerve Tibial	GTEx

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	chr15:41743800-41762200	Weak transcription	Stomach Mucosa	stomach
11	chr15:41744000-41771800	Strong transcription	Fetal Intestine Small	intestine
12	chr15:41744200-41767400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr15:41745200-41766800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:41745200-41775800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:41745800-41754400	Weak transcription	Brain Angular Gyrus	brain
16	chr15:41745800-41763400	Weak transcription	Pancreas	Pancrea
17	chr15:41748000-41761000	Weak transcription	A549	lung
18	chr15:41748600-41756000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:41749200-41753000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr15:41749400-41753000	Strong transcription	Liver	Liver
21	chr15:41749600-41756000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr15:41749800-41753000	Strong transcription	Duodenum Mucosa	Duodenum
23	chr15:41749800-41753000	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr15:41749800-41756000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:41750600-41754600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:41750600-41757400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr15:41750600-41757600	Weak transcription	NHEK	skin
28	chr15:41750600-41761200	Weak transcription	Right Ventricle	heart
29	chr15:41750600-41761800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr15:41750600-41762200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:41750600-41766200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:41750800-41754000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:41750800-41754200	Weak transcription	HSMM	muscle
34	chr15:41750800-41754200	Weak transcription	K562	blood
35	chr15:41750800-41754400	Weak transcription	HepG2	liver
36	chr15:41750800-41754400	Weak transcription	HUVEC	blood vessel
37	chr15:41750800-41754600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:41750800-41755000	Weak transcription	Fetal Kidney	kidney
39	chr15:41750800-41755200	Weak transcription	Fetal Lung	lung
40	chr15:41750800-41755400	Weak transcription	Brain Substantia Nigra	brain
41	chr15:41750800-41755600	Weak transcription	Brain Anterior Caudate	brain
42	chr15:41750800-41755600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:41750800-41757000	Weak transcription	HSMMtube	muscle
44	chr15:41750800-41757200	Weak transcription	Fetal Brain Male	brain
45	chr15:41750800-41757400	Weak transcription	Colonic Mucosa	Colon
46	chr15:41750800-41757400	Weak transcription	Colon Smooth Muscle	Colon
47	chr15:41750800-41758000	Weak transcription	NH-A	brain
48	chr15:41750800-41758200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr15:41750800-41758800	Weak transcription	HMEC	breast
50	chr15:41750800-41759000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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