Variant report

Variant	rs12413113
Chromosome Location	chr10:50759442-50759443
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50746990..50749930-chr10:50758500..50760326,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAT-1	chr10:50759354-50759577	NONHSAT013313

Variant related genes	Relation type
ENSG00000225830	Chromatin interaction
ENSG00000258838	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1012553	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1012554	0.82[ASN][1000 genomes]
rs10776579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10776580	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10857503	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10857505	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11101137	0.81[CHB][hapmap]
rs11101153	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11101154	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11527799	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11527805	0.81[CHB][hapmap]
rs11594945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12161717	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12161719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12218455	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12218602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17177703	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17177717	0.86[CHB][hapmap]
rs17784189	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1880679	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1880680	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1917799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1917822	0.91[ASN][1000 genomes]
rs2222638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2228524	0.82[ASN][1000 genomes]
rs2228528	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2377901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2889771	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750745	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3763728	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3793786	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3793788	0.95[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4012459	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4253013	0.81[CHB][hapmap]
rs4253024	0.82[ASN][1000 genomes]
rs4253043	0.81[CHB][hapmap]
rs4253060	0.81[CHB][hapmap]
rs4253082	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs56002988	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57761316	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59219652	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61288726	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7072155	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7100059	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73315045	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7477098	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv831867	chr10:50607857-50788751	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50755400-50760000	Weak transcription	HSMMtube	muscle
2	chr10:50756200-50761400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr10:50756400-50762000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:50756800-50760800	Enhancers	Muscle Satellite Cultured Cells	--
5	chr10:50757000-50759600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:50757200-50763400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr10:50757400-50760000	Enhancers	Hela-S3	cervix
8	chr10:50757400-50763000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr10:50757400-50763200	Enhancers	NHEK	skin
10	chr10:50757400-50763400	Enhancers	HMEC	breast
11	chr10:50757800-50760000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr10:50757800-50760000	Enhancers	Osteobl	bone
13	chr10:50757800-50761400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:50758000-50760800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr10:50758200-50760200	Enhancers	Placenta	Placenta
16	chr10:50758200-50761200	Enhancers	NH-A	brain
17	chr10:50758400-50759600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr10:50758800-50760000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr10:50759000-50759600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr10:50759000-50760000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr10:50759000-50760200	Enhancers	Aorta	Aorta
22	chr10:50759000-50761000	Enhancers	NHDF-Ad	bronchial
23	chr10:50759200-50759800	Enhancers	HUVEC	blood vessel
24	chr10:50759200-50761400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:50759400-50760000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr10:50759400-50760800	Weak transcription	HSMM	muscle

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