Variant report

Variant	rs62559474
Chromosome Location	chr9:22234936-22234937
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:22234059..22235635-chr9:22238917..22241130,2	MCF-7	breast:
2	chr9:22208810..22215725-chr9:22233777..22241391,18	MCF-7	breast:
3	chr9:22233059..22235536-chr9:22238140..22240172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236921	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11788928	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11790978	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11792798	0.86[EUR][1000 genomes]
rs11792897	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11792932	0.90[EUR][1000 genomes]
rs12003808	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16905769	0.95[EUR][1000 genomes]
rs2025797	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2383209	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2383212	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4461984	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4540492	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4621906	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4644346	0.90[EUR][1000 genomes]
rs62555449	0.81[EUR][1000 genomes]
rs62555450	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62555451	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62555452	0.90[EUR][1000 genomes]
rs62555453	0.85[EUR][1000 genomes]
rs62555455	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62559460	0.90[EUR][1000 genomes]
rs62559467	0.90[EUR][1000 genomes]
rs62559468	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62559469	0.90[EUR][1000 genomes]
rs62559470	0.90[EUR][1000 genomes]
rs62559471	0.90[EUR][1000 genomes]
rs62559472	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62559473	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62559475	1.00[EUR][1000 genomes]
rs62559493	0.91[EUR][1000 genomes]
rs6475620	0.86[EUR][1000 genomes]
rs7035115	0.86[EUR][1000 genomes]
rs73442947	0.86[EUR][1000 genomes]
rs73444955	0.90[EUR][1000 genomes]
rs736723	0.86[EUR][1000 genomes]
rs7848967	0.86[EUR][1000 genomes]
rs7853566	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7859353	0.95[EUR][1000 genomes]
rs7859407	0.90[EUR][1000 genomes]
rs7872728	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs943399	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv892749	chr9:22125913-22244280	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1021264	chr9:22159622-22293804	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1033789	chr9:22183150-22266091	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1016067	chr9:22210874-22432654	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1015364	chr9:22211364-22416886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv540086	chr9:22211364-22416886	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22231200-22237400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr9:22231600-22237600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links