Variant report

Variant	rs2471
Chromosome Location	chr20:22544749-22544750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:8)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:22542551-22545334	HepG2	liver:	n/a	n/a
2	POLR2A	chr20:22544708-22545141	HepG2	liver:	n/a	n/a
3	POLR2A	chr20:22539124-22546431	HepG2	liver:	n/a	n/a
4	POLR2A	chr20:22543786-22545151	HepG2	liver:	n/a	n/a
5	POLR2A	chr20:22539677-22547334	HepG2	liver:	n/a	n/a
6	CEBPB	chr20:22544716-22545032	HepG2	liver:	n/a	chr20:22544870-22544881
7	MBD4	chr20:22543455-22545081	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXA2-2	chr20:22541191-22545754	ENSG00000225074
2	lnc-FOXA2-2	chr20:22544533-22545754	XLOC_013684
3	lnc-FOXA2-2	chr20:22544288-22545754	XLOC_013684
4	lnc-FOXA2-2	chr20:22541194-22545754	XLOC_013684
5	lnc-FOXA2-2	chr20:22540989-22545754	NONHSAT078989
6	lnc-FOXA2-2	chr20:22544533-22545754	NONHSAT078993
7	lnc-FOXA2-2	chr20:22541216-22545754	NONHSAT078994
8	lnc-FOXA2-2	chr20:22541192-22545754	NR_001558

No data

Variant related genes	Relation type
LINC00261	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11087387	0.93[EUR][1000 genomes]
rs11087388	0.84[EUR][1000 genomes]
rs1203868	0.80[EUR][1000 genomes]
rs1203873	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203874	0.93[ASN][1000 genomes]
rs1203875	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203876	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203877	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203883	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203886	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203889	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1203892	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1203894	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1203895	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1203896	0.84[EUR][1000 genomes]
rs1203898	0.81[EUR][1000 genomes]
rs1203899	0.81[AFR][1000 genomes]
rs2277762	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277763	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4815127	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5029909	0.81[EUR][1000 genomes]
rs6036145	0.82[EUR][1000 genomes]
rs6036146	0.95[EUR][1000 genomes]
rs6048183	0.95[EUR][1000 genomes]
rs6048184	0.86[EUR][1000 genomes]
rs6048186	0.98[EUR][1000 genomes]
rs6048191	1.00[CEU][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6048192	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6048196	1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048197	0.84[EUR][1000 genomes]
rs6048199	0.84[EUR][1000 genomes]
rs6048200	0.84[EUR][1000 genomes]
rs6048202	0.82[EUR][1000 genomes]
rs6048205	0.82[CEU][hapmap]
rs73300990	0.84[EUR][1000 genomes]
rs73300993	0.84[EUR][1000 genomes]
rs932560	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs945982	0.87[EUR][1000 genomes];0.82[ASN][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:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22536200-22544800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
2	chr20:22536800-22545200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
3	chr20:22539400-22545200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:22540000-22548800	Weak transcription	Gastric	stomach
5	chr20:22541200-22545000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
6	chr20:22541400-22545200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr20:22542800-22544800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
8	chr20:22542800-22545000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr20:22543200-22548000	Weak transcription	K562	blood
10	chr20:22543400-22545200	Enhancers	Stomach Mucosa	stomach
11	chr20:22543600-22547800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr20:22544000-22545200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr20:22544200-22544800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr20:22544200-22545000	Genic enhancers	Pancreas	Pancrea
15	chr20:22544200-22547000	Genic enhancers	HepG2	liver
16	chr20:22544400-22545000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
17	chr20:22544400-22545000	Bivalent Enhancer	Fetal Lung	lung
18	chr20:22544400-22546400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr20:22544400-22548000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr20:22544600-22549400	Genic enhancers	Liver	Liver

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