Variant report

Variant	rs12219670
Chromosome Location	chr10:50653603-50653604
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	chr10:50648888..50650860-chr10:50652961..50655311,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ERCC6-1	chr10:50641879-50655452	NONHSAT013306

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1012553	0.82[CHB][hapmap]
rs10857494	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857495	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857496	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857498	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857500	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11101133	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11101137	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11101152	0.82[ASN][1000 genomes]
rs11527805	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11594945	0.81[CHB][hapmap]
rs12218602	0.81[CHB][hapmap]
rs12219170	0.82[ASN][1000 genomes]
rs12220085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12221460	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12244804	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12413113	0.81[CHB][hapmap]
rs17177717	0.95[CHB][hapmap];0.85[CHD][hapmap]
rs1917799	0.81[CHB][hapmap]
rs2222638	0.81[CHB][hapmap]
rs2228528	0.86[CHB][hapmap];0.83[MEX][hapmap]
rs2281794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28454254	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3750749	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3793786	0.82[CHB][hapmap]
rs3793788	0.86[CHB][hapmap]
rs3810945	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4253004	0.82[ASN][1000 genomes]
rs4253005	0.86[ASW][hapmap];0.86[YRI][hapmap]
rs4253013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4253040	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4253043	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4253060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4253082	0.86[CHB][hapmap]
rs4253095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4253138	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4253145	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4253215	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4253226	0.82[AMR][1000 genomes]
rs61143747	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7080607	0.82[AMR][1000 genomes]
rs7086144	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73297748	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73305562	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7909342	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv895377	chr10:50588990-50678212	ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50638400-50665800	Weak transcription	Gastric	stomach
2	chr10:50645800-50655200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr10:50648000-50662200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr10:50648000-50662200	Weak transcription	Left Ventricle	heart
5	chr10:50648400-50662200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:50649600-50665600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr10:50650400-50654600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:50650400-50662200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr10:50650400-50662200	Weak transcription	Placenta	Placenta
10	chr10:50650400-50662200	Weak transcription	Pancreas	Pancrea
11	chr10:50650400-50662200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr10:50650800-50654800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:50650800-50662000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:50650800-50662200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:50652000-50654000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:50652200-50653800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:50652200-50662200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr10:50652400-50653800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr10:50652400-50662400	Weak transcription	Aorta	Aorta
20	chr10:50653200-50653800	Enhancers	Primary hematopoietic stem cells	blood
21	chr10:50653200-50654000	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links