Variant report

Variant	rs11676678
Chromosome Location	chr2:55996959-55996960
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55994825..55997779-chr2:55998633..56001283,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11125600	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11684982	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693187	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11694759	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11694790	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887339	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12614845	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404193	0.95[ASN][1000 genomes]
rs1430198	0.95[ASN][1000 genomes]
rs1430199	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430200	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465624	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465625	0.90[ASN][1000 genomes]
rs1961386	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4233963	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4671259	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4672069	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6723918	0.95[ASN][1000 genomes]
rs6742316	0.91[ASN][1000 genomes]
rs6747885	0.83[ASN][1000 genomes]
rs6761334	0.89[ASN][1000 genomes]
rs7560508	0.95[ASN][1000 genomes]
rs7577894	0.89[ASN][1000 genomes]
rs9309269	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309270	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs934274	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs934275	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs934276	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934277	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv999962	chr2:55976574-56011517	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv997683	chr2:55976574-56013875	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv431080	chr2:55988293-56011517	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55989400-55997800	Weak transcription	Ovary	ovary
2	chr2:55989400-56015000	Weak transcription	Aorta	Aorta
3	chr2:55990000-55998400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:55994200-55998200	Weak transcription	HUVEC	blood vessel
5	chr2:55995600-55997400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:55995800-55997000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:55996000-55997000	Enhancers	HMEC	breast
8	chr2:55996000-55997000	Enhancers	NHEK	skin
9	chr2:55996000-55997200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:55996000-55997200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:55996200-55997000	Enhancers	HSMM	muscle
12	chr2:55996400-55999200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:55996400-55999200	Weak transcription	Osteobl	bone
14	chr2:55996800-55999000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:55996800-55999400	Weak transcription	Muscle Satellite Cultured Cells	--

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