Variant report

Variant	rs2277762
Chromosome Location	chr20:22548283-22548284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:22547089-22548440	H1-neurons	neurons:	n/a	n/a
2	SUZ12	chr20:22547785-22550361	NT2-D1	testis:	n/a	n/a
3	EBF1	chr20:22548083-22548373	GM12878	blood:	n/a	chr20:22548266-22548275 chr20:22548265-22548276
4	POLR2A	chr20:22548261-22548719	HepG2	liver:	n/a	n/a
5	POLR2A	chr20:22547566-22548500	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:22537625..22541473-chr20:22546828..22550085,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXA2-2	chr20:22547321-22548523	NONHSAT078988

Variant related genes	Relation type
LINC00261	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11087387	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11087388	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203873	0.95[EUR][1000 genomes]
rs1203875	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1203876	0.95[EUR][1000 genomes]
rs1203877	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1203879	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1203880	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1203881	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1203883	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1203884	1.00[CEU][hapmap];0.90[CHD][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1203886	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1203889	0.95[EUR][1000 genomes]
rs1203892	0.93[EUR][1000 genomes]
rs1203894	0.93[EUR][1000 genomes]
rs1203895	0.83[EUR][1000 genomes]
rs1203905	0.87[TSI][hapmap]
rs1203907	0.87[TSI][hapmap]
rs1337919	0.86[TSI][hapmap]
rs2277763	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471	1.00[CEU][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4815127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5029909	0.82[EUR][1000 genomes]
rs6036145	0.87[EUR][1000 genomes]
rs6036146	1.00[EUR][1000 genomes]
rs6036152	0.81[EUR][1000 genomes]
rs6048183	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6048184	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6048186	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6048191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6048192	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6048196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048197	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048199	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048200	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048202	0.87[EUR][1000 genomes]
rs6048205	0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6048206	0.93[TSI][hapmap]
rs6048209	0.86[TSI][hapmap]
rs73300990	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73300993	0.89[EUR][1000 genomes]
rs932560	0.93[EUR][1000 genomes]
rs945982	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428690	chr20:22528757-22649625	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22540000-22548800	Weak transcription	Gastric	stomach
2	chr20:22544600-22549400	Genic enhancers	Liver	Liver
3	chr20:22545600-22548600	Weak transcription	Pancreas	Pancrea
4	chr20:22546600-22548800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr20:22547000-22548400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
6	chr20:22547000-22550800	Strong transcription	HepG2	liver
7	chr20:22547200-22549000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr20:22547800-22549800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr20:22548000-22548400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
10	chr20:22548000-22548400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr20:22548000-22548600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
12	chr20:22548000-22548600	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr20:22548000-22549000	Enhancers	K562	blood
14	chr20:22548000-22549200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr20:22548200-22548400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
16	chr20:22548200-22548400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
17	chr20:22548200-22548800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
18	chr20:22548200-22549000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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