Variant report

Variant	rs12220558
Chromosome Location	chr10:1573754-1573755
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	chr10:1462956..1463735-chr10:1573069..1574036,3	MCF-7	breast:
2	chr10:1568642..1571276-chr10:1573418..1576224,2	K562	blood:

Variant related genes	Relation type
ENSG00000205696	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10794754	0.86[ASN][1000 genomes]
rs10794756	0.81[ASN][1000 genomes]
rs10903472	0.86[ASN][1000 genomes]
rs10903473	0.86[ASN][1000 genomes]
rs10903477	0.81[ASN][1000 genomes]
rs10903478	0.81[ASN][1000 genomes]
rs10903479	0.81[ASN][1000 genomes]
rs11250593	0.87[ASN][1000 genomes]
rs11250594	0.87[ASN][1000 genomes]
rs11250596	0.86[ASN][1000 genomes]
rs11250597	0.86[ASN][1000 genomes]
rs11250600	0.86[ASN][1000 genomes]
rs11250607	0.81[ASN][1000 genomes]
rs11250608	0.81[ASN][1000 genomes]
rs11250609	0.81[ASN][1000 genomes]
rs11250610	0.81[ASN][1000 genomes]
rs11250613	0.81[ASN][1000 genomes]
rs11250614	0.81[ASN][1000 genomes]
rs11250615	0.81[ASN][1000 genomes]
rs11250616	0.81[ASN][1000 genomes]
rs12220566	0.93[ASN][1000 genomes]
rs12244289	0.82[ASN][1000 genomes]
rs12412937	0.81[ASN][1000 genomes]
rs2138691	0.89[ASN][1000 genomes]
rs2138692	0.84[ASN][1000 genomes]
rs2676732	0.94[ASN][1000 genomes]
rs2676733	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2676776	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2676778	0.93[ASN][1000 genomes]
rs2813453	0.93[ASN][1000 genomes]
rs2813458	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2813460	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2813461	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2944604	0.81[EUR][1000 genomes]
rs34032124	0.87[ASN][1000 genomes]
rs4253993	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4376829	0.86[ASN][1000 genomes]
rs4880864	0.81[ASN][1000 genomes]
rs61831943	0.81[ASN][1000 genomes]
rs7079988	0.94[ASN][1000 genomes]
rs7080610	0.81[ASN][1000 genomes]
rs7082956	0.93[ASN][1000 genomes]
rs7903267	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer 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 target site	39 gene(s)	inside rSNPs	diseases
3	nsv1041498	chr10:1117200-1760190	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1052682	chr10:1162925-1675641	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1043944	chr10:1168095-1626019	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv540411	chr10:1168095-1626019	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1046041	chr10:1195214-2189155	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1037054	chr10:1232041-1865296	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv540413	chr10:1232041-1865296	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv549769	chr10:1244020-1764966	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv549786	chr10:1293100-1904598	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv894736	chr10:1513349-1672408	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1054555	chr10:1558145-1965145	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv894737	chr10:1560338-1692796	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:1565800-1578000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:1568400-1577200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:1572000-1575000	Enhancers	Fetal Thymus	thymus
4	chr10:1572600-1575000	Genic enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links