Variant report

Variant	rs1960628
Chromosome Location	chr3:110687376-110687377
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1020891	1.00[EUR][1000 genomes]
rs1037960	1.00[EUR][1000 genomes]
rs1160101	1.00[EUR][1000 genomes]
rs11929276	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1350928	1.00[EUR][1000 genomes]
rs1350931	1.00[EUR][1000 genomes]
rs1381827	1.00[EUR][1000 genomes]
rs1381829	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1462791	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1462792	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1462796	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1462806	1.00[EUR][1000 genomes]
rs1580287	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1599575	1.00[EUR][1000 genomes]
rs1599577	1.00[EUR][1000 genomes]
rs1599665	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1841734	1.00[EUR][1000 genomes]
rs1903758	1.00[EUR][1000 genomes]
rs1975901	1.00[EUR][1000 genomes]
rs1993801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2054376	1.00[EUR][1000 genomes]
rs2061682	1.00[EUR][1000 genomes]
rs2169566	1.00[EUR][1000 genomes]
rs3957571	1.00[EUR][1000 genomes]
rs3957572	1.00[EUR][1000 genomes]
rs4305447	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4549301	1.00[EUR][1000 genomes]
rs4593059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682021	1.00[EUR][1000 genomes]
rs4682216	1.00[EUR][1000 genomes]
rs4682218	1.00[EUR][1000 genomes]
rs4682220	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682233	0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs4682236	1.00[EUR][1000 genomes]
rs4682237	1.00[EUR][1000 genomes]
rs4682241	1.00[EUR][1000 genomes]
rs58106260	1.00[EUR][1000 genomes]
rs58423117	1.00[EUR][1000 genomes]
rs61035297	1.00[EUR][1000 genomes]
rs6437932	1.00[EUR][1000 genomes]
rs6437935	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6437936	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6437956	1.00[EUR][1000 genomes]
rs6765553	1.00[EUR][1000 genomes]
rs6794368	1.00[EUR][1000 genomes]
rs72935984	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72935992	1.00[EUR][1000 genomes]
rs72937908	1.00[EUR][1000 genomes]
rs72937909	1.00[EUR][1000 genomes]
rs72937912	1.00[EUR][1000 genomes]
rs72937914	1.00[EUR][1000 genomes]
rs72937920	1.00[EUR][1000 genomes]
rs72937925	1.00[EUR][1000 genomes]
rs72937928	1.00[EUR][1000 genomes]
rs72937936	1.00[EUR][1000 genomes]
rs72937963	1.00[EUR][1000 genomes]
rs72937977	1.00[EUR][1000 genomes]
rs72937981	1.00[EUR][1000 genomes]
rs7609772	1.00[EUR][1000 genomes]
rs7618482	1.00[EUR][1000 genomes]
rs7619492	1.00[EUR][1000 genomes]
rs7619978	1.00[EUR][1000 genomes]
rs7628011	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7628921	1.00[EUR][1000 genomes]
rs7634788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7637704	1.00[EUR][1000 genomes]
rs7641469	1.00[EUR][1000 genomes]
rs7642037	1.00[EUR][1000 genomes]
rs7644614	1.00[EUR][1000 genomes]
rs7650020	1.00[EUR][1000 genomes]
rs898974	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9288915	1.00[EUR][1000 genomes]
rs931024	1.00[EUR][1000 genomes]
rs964444	1.00[EUR][1000 genomes]
rs9823218	1.00[EUR][1000 genomes]
rs9826523	1.00[EUR][1000 genomes]
rs9830162	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9835919	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9856917	1.00[EUR][1000 genomes]
rs9860353	1.00[EUR][1000 genomes]
rs9869379	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs988374	1.00[EUR][1000 genomes]
rs990256	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs992130	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1014199	chr3:110293896-110754155	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv829674	chr3:110616256-110771049	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110683800-110703000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:110685000-110687800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:110685000-110688200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:110685600-110688800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:110685800-110689000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:110686000-110690400	Active TSS	H1 Cell Line	embryonic stem cell

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