Variant report

Variant	rs4820938
Chromosome Location	chr22:31508683-31508684
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	SP1	chr22:31508584-31509003	GM12878	blood:	n/a	n/a
2	NFYB	chr22:31508594-31508989	Hela-S3	cervix:	n/a	chr22:31508802-31508817 chr22:31508761-31508776
3	SP1	chr22:31508593-31508925	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD2	chr22:31508673-31508808	H1-hESC	embryonic stem cell:	n/a	n/a
5	NFYA	chr22:31508564-31508971	K562	blood:	n/a	chr22:31508707-31508725 chr22:31508731-31508749 chr22:31508755-31508773
6	NFYB	chr22:31508564-31509023	GM12878	blood:	n/a	chr22:31508802-31508817 chr22:31508761-31508776
7	NFYB	chr22:31508496-31509091	K562	blood:	n/a	chr22:31508802-31508817 chr22:31508761-31508776
8	SP1	chr22:31508468-31508986	K562	blood:	n/a	n/a
9	SP1	chr22:31508672-31509011	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000235573	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1004243	0.86[YRI][hapmap];0.80[AFR][1000 genomes]
rs11089488	0.83[AFR][1000 genomes]
rs11089489	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11703403	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11703478	0.81[AFR][1000 genomes]
rs11705137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12167220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12170688	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12330010	0.82[AFR][1000 genomes]
rs13053329	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13054770	0.83[AFR][1000 genomes]
rs1807739	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35657209	0.81[AFR][1000 genomes]
rs4820939	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820941	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62236155	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8135353	1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs9621184	1.00[CHB][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs9621185	1.00[CHB][hapmap];0.80[AFR][1000 genomes]
rs9621187	0.80[AFR][1000 genomes]
rs9621188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9896	chr22:31369204-31513933	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv914975	chr22:31466083-31514477	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv914976	chr22:31475307-31543260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv914977	chr22:31477563-31514477	Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv964621	chr22:31503851-31509520	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31504200-31515000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr22:31504200-31515400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr22:31504400-31517800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr22:31504400-31518000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr22:31504600-31518600	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links