Variant report

Variant	rs10499138
Chromosome Location	chr6:128492182-128492183
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128485115..128487072-chr6:128489971..128492431,2	K562	blood:
2	chr6:128484630..128487513-chr6:128490490..128493192,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10046162	0.82[EUR][1000 genomes]
rs10485161	1.00[EUR][1000 genomes]
rs10485162	1.00[EUR][1000 genomes]
rs10499136	0.82[EUR][1000 genomes]
rs10499137	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10872329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11961776	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11962214	1.00[JPT][hapmap]
rs11962916	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11965115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11967302	0.82[ASN][1000 genomes]
rs11968433	1.00[EUR][1000 genomes]
rs11970637	1.00[EUR][1000 genomes]
rs12110357	1.00[JPT][hapmap]
rs12110728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17053270	1.00[EUR][1000 genomes]
rs17055270	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17055274	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17055283	0.91[ASN][1000 genomes]
rs17055285	0.91[ASN][1000 genomes]
rs17055290	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17055300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055360	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055365	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17055403	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055412	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17055415	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055421	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17055445	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17055461	1.00[EUR][1000 genomes]
rs17055488	1.00[EUR][1000 genomes]
rs17055499	1.00[EUR][1000 genomes]
rs17055501	1.00[EUR][1000 genomes]
rs17055507	1.00[EUR][1000 genomes]
rs1738273	1.00[EUR][1000 genomes]
rs1768358	1.00[EUR][1000 genomes]
rs1856497	1.00[EUR][1000 genomes]
rs28874136	0.82[EUR][1000 genomes]
rs3923033	0.82[ASN][1000 genomes]
rs4072328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4131020	1.00[EUR][1000 genomes]
rs41439546	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4440487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4496822	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4498385	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4895830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4895832	1.00[EUR][1000 genomes]
rs4897244	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897246	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897247	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897248	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897250	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55828045	1.00[EUR][1000 genomes]
rs56042959	1.00[EUR][1000 genomes]
rs56932458	1.00[EUR][1000 genomes]
rs57797601	1.00[EUR][1000 genomes]
rs58652879	1.00[EUR][1000 genomes]
rs58706847	1.00[EUR][1000 genomes]
rs59341107	0.90[EUR][1000 genomes]
rs59636446	0.91[ASN][1000 genomes]
rs60264538	1.00[EUR][1000 genomes]
rs60436012	1.00[EUR][1000 genomes]
rs61111040	1.00[EUR][1000 genomes]
rs6900798	1.00[EUR][1000 genomes]
rs6904354	0.82[ASN][1000 genomes]
rs6905735	1.00[EUR][1000 genomes]
rs6909380	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910587	1.00[EUR][1000 genomes]
rs6913738	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6918772	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929394	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929623	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933133	1.00[EUR][1000 genomes]
rs6935188	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6938199	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73584655	0.83[ASN][1000 genomes]
rs73584673	0.91[ASN][1000 genomes]
rs73586607	0.82[ASN][1000 genomes]
rs73586609	0.82[ASN][1000 genomes]
rs73586611	0.82[ASN][1000 genomes]
rs73586613	0.82[ASN][1000 genomes]
rs73588647	0.82[ASN][1000 genomes]
rs73588698	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73590666	1.00[EUR][1000 genomes]
rs73592613	1.00[EUR][1000 genomes]
rs73592686	1.00[EUR][1000 genomes]
rs73773990	0.82[EUR][1000 genomes]
rs7746783	1.00[JPT][hapmap]
rs7751187	1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7752113	0.82[EUR][1000 genomes]
rs7754321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7754637	1.00[EUR][1000 genomes]
rs7768121	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769070	1.00[JPT][hapmap]
rs7772200	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9491909	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv604643	chr6:128359362-128493991	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv886650	chr6:128403745-128513395	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1031827	chr6:128418702-128497881	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv528869	chr6:128421762-128496557	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv604646	chr6:128421762-128531651	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv604647	chr6:128421762-128547177	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv886651	chr6:128450019-128565778	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv886652	chr6:128455539-128496557	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv886653	chr6:128455539-128555805	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv886654	chr6:128471938-128555805	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Hearing impairment	20068591	GWAS catalog

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128452600-128505200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:128461400-128504400	Weak transcription	Fetal Intestine Large	intestine
3	chr6:128465600-128504400	Weak transcription	Fetal Thymus	thymus
4	chr6:128465600-128523200	Weak transcription	Left Ventricle	heart
5	chr6:128466200-128494000	Weak transcription	Fetal Heart	heart
6	chr6:128469400-128496200	Weak transcription	HepG2	liver
7	chr6:128472400-128494200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:128477800-128504200	Weak transcription	HSMM	muscle
9	chr6:128480200-128494000	Weak transcription	NH-A	brain
10	chr6:128487200-128494200	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:128487400-128494000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:128488200-128508000	Weak transcription	Aorta	Aorta
13	chr6:128488200-128565200	Weak transcription	Fetal Stomach	stomach
14	chr6:128489000-128492800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr6:128489000-128507800	Weak transcription	NHLF	lung
16	chr6:128489600-128493800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:128489600-128505200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:128489800-128494000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:128489800-128494000	Weak transcription	Right Atrium	heart
20	chr6:128489800-128494000	Weak transcription	HMEC	breast
21	chr6:128489800-128494000	Weak transcription	NHEK	skin
22	chr6:128489800-128504600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:128489800-128514200	Weak transcription	Gastric	stomach
24	chr6:128490000-128494000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:128490000-128496000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr6:128490000-128498600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:128490000-128511600	Weak transcription	Pancreas	Pancrea
28	chr6:128490000-128520200	Weak transcription	Fetal Intestine Small	intestine
29	chr6:128490400-128492200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:128491400-128492800	Strong transcription	Primary B cells from cord blood	blood

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