Variant report

Variant	rs6531236
Chromosome Location	chr2:20587965-20587966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20587063..20590081-chr2:20645437..20648292,3	MCF-7	breast:
2	chr2:20587207..20591991-chr2:20644052..20649862,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10209568	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11901184	0.87[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs12464277	0.87[ASN][1000 genomes]
rs1476941	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1985318	0.82[ASN][1000 genomes]
rs1985319	0.87[ASN][1000 genomes]
rs2348705	0.87[ASN][1000 genomes]
rs343138	0.88[ASN][1000 genomes]
rs343140	0.87[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343142	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs343143	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs343144	0.92[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs343147	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs343151	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs343152	0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[ASN][1000 genomes]
rs343154	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs343161	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs4666306	0.87[ASN][1000 genomes]
rs4666386	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4666387	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4666389	0.87[ASN][1000 genomes]
rs4666390	0.87[ASN][1000 genomes]
rs62124612	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6705947	0.87[ASN][1000 genomes]
rs67511352	0.85[ASN][1000 genomes]
rs725490	0.81[ASN][1000 genomes]
rs7563890	0.87[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs7564799	0.87[ASN][1000 genomes]
rs7564810	0.87[ASN][1000 genomes]
rs7576439	0.87[ASN][1000 genomes]
rs7576806	0.87[ASN][1000 genomes]
rs7603518	0.87[ASN][1000 genomes]
rs7604195	0.88[ASN][1000 genomes]
rs953927	0.87[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873716	chr2:20572094-20621404	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv581165	chr2:20581058-20616990	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20581600-20601000	Weak transcription	Right Atrium	heart
2	chr2:20585800-20593800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:20586600-20589800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:20586600-20592000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:20587200-20591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:20587600-20588600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr2:20587800-20591600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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