Variant report

Variant	rs2050065
Chromosome Location	chr1:71510419-71510420
allele	G/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	IRF1	chr1:71510332-71511099	K562	blood:	n/a	n/a
2	MYC	chr1:71510359-71511699	K562	blood:	n/a	chr1:71511075-71511082 chr1:71511074-71511083
3	JUN	chr1:71510171-71511032	K562	blood:	n/a	n/a
4	ARID3A	chr1:71510208-71510932	K562	blood:	n/a	n/a
5	ZNF384	chr1:71509922-71510937	K562	blood:	n/a	n/a
6	RCOR1	chr1:71510395-71511637	K562	blood:	n/a	n/a
7	EP300	chr1:71510396-71510962	K562	blood:	n/a	chr1:71510590-71510600

No.	Distal block	Cell Line	Cell type
1	chr1:71217715..71220280-chr1:71509356..71511477,2	K562	blood:
2	chr1:71240165..71242218-chr1:71510173..71512188,2	K562	blood:
3	chr1:71164353..71167028-chr1:71509072..71511419,2	K562	blood:
4	chr1:71509104..71511027-chr1:71511341..71513340,2	MCF-7	breast:
5	chr1:71113661..71115986-chr1:71510232..71513062,3	K562	blood:

Variant related genes	Relation type
ZRANB2-AS1	TF binding region
ENSG00000050628	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1005749	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10789314	1.00[CHB][hapmap]
rs10889906	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10889907	1.00[ASN][1000 genomes]
rs12119848	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12122320	0.89[ASN][1000 genomes]
rs12131077	0.89[ASN][1000 genomes]
rs12131515	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12142055	0.89[ASN][1000 genomes]
rs12145536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12145635	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1474663	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2206344	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2744897	0.89[ASN][1000 genomes]
rs2744898	0.89[ASN][1000 genomes]
rs2744900	0.89[ASN][1000 genomes]
rs2744906	0.89[ASN][1000 genomes]
rs2744907	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2744908	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2744918	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs3000466	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs479934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs481940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs496483	0.84[EUR][1000 genomes]
rs510414	0.80[GIH][hapmap]
rs61777272	0.89[ASN][1000 genomes]
rs61777274	0.89[ASN][1000 genomes]
rs61778911	1.00[ASN][1000 genomes]
rs61778912	0.89[ASN][1000 genomes]
rs6424415	0.89[ASN][1000 genomes]
rs647921	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs651265	0.80[GIH][hapmap]
rs72671095	0.89[ASN][1000 genomes]
rs726764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7529930	1.00[ASN][1000 genomes]
rs847704	0.80[GIH][hapmap]
rs880099	1.00[ASN][1000 genomes]
rs9970600	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9970739	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	esv1845198	chr1:71274759-71514969	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv546472	chr1:71432984-71541003	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	555 gene(s)	inside rSNPs	diseases
3	esv1850593	chr1:71444149-71514969	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv871242	chr1:71481050-71519326	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2050065	SERBP1	cis	parietal	SCAN
rs2050065	TNNI3K	cis	cerebellum	SCAN
rs2050065	TNNI3K	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:71497600-71510600	Weak transcription	Aorta	Aorta
2	chr1:71503000-71511200	Weak transcription	Pancreas	Pancrea
3	chr1:71505000-71511200	Weak transcription	Gastric	stomach
4	chr1:71508400-71510600	Weak transcription	NHDF-Ad	bronchial
5	chr1:71508800-71512400	Active TSS	K562	blood
6	chr1:71509000-71512200	Active TSS	Adipose Nuclei	Adipose
7	chr1:71510200-71511400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:71510400-71510600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:71510400-71510600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:71510400-71511000	Active TSS	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links