Variant report

Variant	rs7163649
Chromosome Location	chr15:41586798-41586799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41576500..41578232-chr15:41585051..41586799,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10152497	0.88[ASN][1000 genomes]
rs10152702	0.81[ASN][1000 genomes]
rs10153010	0.88[ASN][1000 genomes]
rs10467974	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10518718	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11549913	0.87[ASN][1000 genomes]
rs11630191	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11631770	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.85[ASN][1000 genomes]
rs11633799	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852609	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11857631	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12324291	0.91[ASN][1000 genomes]
rs13379756	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs16971767	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16971798	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16971806	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16971832	0.91[JPT][hapmap]
rs16971834	0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap]
rs1757463	0.87[CHB][hapmap]
rs2015781	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2777491	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs28393472	0.88[ASN][1000 genomes]
rs28526381	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28557159	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs28578057	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28583065	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28600680	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28643296	0.95[ASN][1000 genomes]
rs28655070	0.81[ASN][1000 genomes]
rs28716108	0.93[ASN][1000 genomes]
rs28792672	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs316605	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs316609	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs316610	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs316613	0.82[ASN][1000 genomes]
rs316614	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs35826725	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3743038	0.95[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55782852	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58335029	0.91[ASN][1000 genomes]
rs58910172	0.95[ASN][1000 genomes]
rs59590312	0.90[ASN][1000 genomes]
rs61037359	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61127691	0.95[ASN][1000 genomes]
rs6650519	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66538814	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7161772	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7163788	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7165675	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167498	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7167729	0.87[ASN][1000 genomes]
rs7168177	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7168307	0.82[GIH][hapmap];0.84[MEX][hapmap]
rs7172148	0.82[ASN][1000 genomes]
rs7175690	0.95[ASN][1000 genomes]
rs7175800	0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7176314	0.95[ASN][1000 genomes]
rs7176505	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7176588	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177641	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs7178634	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7178777	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]
rs7180418	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs7181560	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7181911	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7182667	0.91[ASN][1000 genomes]
rs7182700	0.82[ASN][1000 genomes]
rs7183337	0.91[ASN][1000 genomes]
rs73404980	0.88[ASN][1000 genomes]
rs73404987	0.93[ASN][1000 genomes]
rs73404994	0.88[ASN][1000 genomes]
rs73404995	0.88[ASN][1000 genomes]
rs73404996	0.88[ASN][1000 genomes]
rs73405000	0.86[ASN][1000 genomes]
rs73405001	0.86[ASN][1000 genomes]
rs73407109	0.88[ASN][1000 genomes]
rs8023530	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs8023619	0.93[ASN][1000 genomes]
rs8026197	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8027626	0.87[ASN][1000 genomes]
rs8032838	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034626	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8034819	0.82[ASN][1000 genomes]
rs8036498	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8037574	0.83[GIH][hapmap];0.84[MEX][hapmap]
rs8037824	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8041325	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs823716	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs919961	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9302109	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9672866	0.84[ASN][1000 genomes]
rs9972288	0.89[ASN][1000 genomes]
rs9972547	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045455	chr15:41536624-41620534	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	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
4	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers 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

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs7163649	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs7163649	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs7163649	NDUFAF1	cis	multi-tissue	Pritchard
rs7163649	OIP5-AS1	cis	Esophagus Muscularis	GTEx
rs7163649	NDUFAF1	cis	parietal	SCAN
rs7163649	NUSAP1	cis	cerebellum	SCAN
rs7163649	RPAP1	cis	parietal	SCAN
rs7163649	OIP5-AS1	cis	Nerve Tibial	GTEx
rs7163649	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs7163649	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs7163649	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs7163649	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs7163649	OIP5-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs7163649	NDUFAF1	cis	Muscle Skeletal	GTEx
rs7163649	NDUFAF1	cis	lymphoblastoid	seeQTL
rs7163649	NDUFAF1	cis	Thyroid	GTEx
rs7163649	NDUFAF1	cis	cerebellum	SCAN
rs7163649	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs7163649	OIP5-AS1	cis	Artery Tibial	GTEx
rs7163649	NUSAP1	cis	parietal	SCAN
rs7163649	CASC5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41577400-41610600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41577600-41606400	Weak transcription	Stomach Mucosa	stomach
3	chr15:41577800-41589000	Weak transcription	Esophagus	oesophagus
4	chr15:41577800-41591600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:41578000-41588400	Weak transcription	Right Atrium	heart
6	chr15:41578000-41591600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:41578200-41591800	Strong transcription	Fetal Stomach	stomach
8	chr15:41578200-41592600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:41578400-41592600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:41578800-41587800	Strong transcription	Fetal Muscle Leg	muscle
11	chr15:41578800-41591800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:41579200-41593200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:41579200-41612400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:41580000-41592600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:41580600-41603200	Weak transcription	Psoas Muscle	Psoas
16	chr15:41581000-41588400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:41581000-41590000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:41581000-41593200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:41581200-41586800	Weak transcription	Fetal Heart	heart
20	chr15:41581200-41586800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:41581200-41587000	Weak transcription	Brain Germinal Matrix	brain
22	chr15:41581200-41587600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:41581200-41588200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:41581200-41589000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:41581200-41589000	Weak transcription	Ovary	ovary
26	chr15:41581200-41589000	Weak transcription	Spleen	Spleen
27	chr15:41581200-41589000	Weak transcription	HSMMtube	muscle
28	chr15:41581200-41589200	Weak transcription	Colonic Mucosa	Colon
29	chr15:41581200-41589200	Weak transcription	Pancreas	Pancrea
30	chr15:41581200-41592200	Weak transcription	Brain Angular Gyrus	brain
31	chr15:41581200-41592200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:41581200-41592400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:41581200-41593000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:41581200-41595200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr15:41581200-41596000	Weak transcription	Small Intestine	intestine
36	chr15:41581200-41598400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:41581200-41601400	Weak transcription	NHDF-Ad	bronchial
38	chr15:41581200-41602200	Weak transcription	Brain Hippocampus Middle	brain
39	chr15:41581200-41602600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr15:41581200-41604800	Weak transcription	Gastric	stomach
41	chr15:41581200-41605000	Weak transcription	Brain Substantia Nigra	brain
42	chr15:41581200-41607000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr15:41581200-41609600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:41581200-41623600	Weak transcription	Fetal Brain Male	brain
45	chr15:41581400-41589200	Weak transcription	HUVEC	blood vessel
46	chr15:41581400-41605000	Weak transcription	HMEC	breast
47	chr15:41581400-41610400	Weak transcription	NHLF	lung
48	chr15:41581600-41588400	Strong transcription	Dnd41	blood
49	chr15:41581600-41589000	Weak transcription	Brain Anterior Caudate	brain
50	chr15:41581600-41589200	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links