Variant report

Variant	rs10509558
Chromosome Location	chr10:90666033-90666034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1029024	0.82[CHB][hapmap]
rs10509555	1.00[EUR][1000 genomes]
rs10509556	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs10509559	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509560	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap]
rs11202882	0.93[YRI][hapmap]
rs11202884	0.86[YRI][hapmap]
rs11202885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202906	0.91[CHB][hapmap]
rs11202907	0.91[CHB][hapmap]
rs12240659	0.92[AFR][1000 genomes]
rs12241898	0.81[MKK][hapmap]
rs12242274	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12245057	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12245122	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12245525	1.00[EUR][1000 genomes]
rs12245668	1.00[EUR][1000 genomes]
rs12247227	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs12254451	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12257540	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12258025	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12260182	0.86[YRI][hapmap]
rs12260572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261664	0.86[ASN][1000 genomes]
rs12262461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12263461	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12264840	0.91[CHB][hapmap]
rs12266049	0.86[YRI][hapmap]
rs12266993	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12413277	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12414800	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113311	1.00[EUR][1000 genomes]
rs17113344	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17113363	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113426	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17113457	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113476	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113724	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113959	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114000	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114016	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114020	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114057	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114116	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap]
rs17114143	0.90[CHB][hapmap]
rs17114186	0.91[CHB][hapmap]
rs17114283	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap]
rs2119685	0.91[CHB][hapmap]
rs2231780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231786	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282122	1.00[EUR][1000 genomes]
rs35996190	1.00[EUR][1000 genomes]
rs3781206	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap]
rs3781208	0.91[CHB][hapmap]
rs3814691	0.82[CHB][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3816245	0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[TSI][hapmap]
rs3898173	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898174	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56998609	1.00[EUR][1000 genomes]
rs58673564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58986570	1.00[EUR][1000 genomes]
rs59661152	1.00[EUR][1000 genomes]
rs60349051	1.00[EUR][1000 genomes]
rs60523093	1.00[EUR][1000 genomes]
rs7070713	0.91[CHB][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs7077019	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7078383	0.91[CHB][hapmap]
rs7085698	0.91[CHB][hapmap]
rs7090604	1.00[EUR][1000 genomes]
rs7090631	0.91[CHB][hapmap]
rs7098235	0.91[CHB][hapmap]
rs7098246	1.00[EUR][1000 genomes]
rs73364839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73364841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73364851	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74150103	0.86[ASN][1000 genomes]
rs7897521	0.91[CHB][hapmap]
rs7908852	0.91[CHB][hapmap];1.00[TSI][hapmap]
rs7913997	1.00[EUR][1000 genomes]
rs7915393	0.91[CHB][hapmap]
rs9804254	1.00[YRI][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr10:90647400-90675200	Weak transcription	Spleen	Spleen
4	chr10:90647400-90681000	Weak transcription	Aorta	Aorta
5	chr10:90654000-90687400	Weak transcription	Right Ventricle	heart
6	chr10:90655200-90675200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:90655200-90701400	Weak transcription	Gastric	stomach
8	chr10:90657400-90667800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:90657400-90668000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr10:90657400-90676200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr10:90657600-90670600	Weak transcription	Liver	Liver
12	chr10:90657600-90675400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr10:90657600-90677600	Weak transcription	Lung	lung
14	chr10:90657600-90686400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr10:90658000-90668200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr10:90658000-90672800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr10:90658600-90686000	Weak transcription	Brain Anterior Caudate	brain
18	chr10:90659600-90689800	Weak transcription	Esophagus	oesophagus
19	chr10:90660400-90674200	Strong transcription	Primary T cells from cord blood	blood
20	chr10:90660400-90695000	Weak transcription	Fetal Brain Male	brain
21	chr10:90660600-90688200	Strong transcription	Dnd41	blood
22	chr10:90661000-90666800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr10:90661000-90669400	Strong transcription	Hela-S3	cervix
24	chr10:90661200-90676200	Strong transcription	Fetal Thymus	thymus
25	chr10:90661400-90667400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr10:90661400-90667400	Strong transcription	A549	lung
27	chr10:90661400-90669000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr10:90661600-90678400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:90661600-90687600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr10:90661600-90688800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr10:90661600-90692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:90661800-90674200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr10:90662000-90667800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr10:90662000-90676200	Weak transcription	NH-A	brain
35	chr10:90662000-90683000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr10:90662200-90667200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr10:90662200-90668600	Strong transcription	Primary hematopoietic stem cells	blood
38	chr10:90662200-90668600	Strong transcription	HSMM	muscle
39	chr10:90662200-90672000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr10:90662200-90672800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr10:90662200-90672800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:90662400-90666800	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr10:90662400-90670000	Weak transcription	HMEC	breast
44	chr10:90662400-90671800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr10:90662600-90666400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr10:90662600-90687600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr10:90662800-90671600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr10:90662800-90688800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr10:90663200-90668600	Strong transcription	Osteobl	bone
50	chr10:90663200-90674200	Strong transcription	GM12878-XiMat	blood

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