Variant report

Variant	rs11172072
Chromosome Location	chr12:57331591-57331592
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	ZNF263	chr12:57331334-57331602	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57330845..57332526-chr12:57336068..57338551,2	MCF-7	breast:
2	chr12:57323485..57328382-chr12:57328704..57333004,6	K562	blood:
3	chr12:57322265..57324003-chr12:57330480..57332983,2	MCF-7	breast:
4	chr12:57325326..57326887-chr12:57330449..57332916,2	K562	blood:

Variant related genes	Relation type
SDR9C7	TF binding region
ENSG00000170426	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1072669	0.94[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876960	0.94[CEU][hapmap];0.85[CHB][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172071	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172076	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1601405	0.94[CEU][hapmap];0.86[CHB][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1825514	0.83[CEU][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1872436	0.86[ASN][1000 genomes]
rs2629413	0.87[ASN][1000 genomes]
rs3782331	0.94[CEU][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57926126	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58009868	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59665366	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60101051	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs719749	0.88[ASN][1000 genomes]
rs719750	0.88[ASN][1000 genomes]
rs7314151	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7314262	0.94[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7970701	0.86[ASN][1000 genomes]
rs840160	0.86[ASN][1000 genomes]
rs840162	0.87[ASN][1000 genomes]
rs840163	0.82[ASN][1000 genomes]
rs863459	0.88[ASN][1000 genomes]
rs864541	0.88[ASN][1000 genomes]
rs901069	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv1043846	chr12:57323709-57377509	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv12940	chr12:57331182-57379580	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv1051116	chr12:57331370-57380365	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	esv10544	chr12:57331527-57352203	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57325800-57335200	Weak transcription	Fetal Intestine Large	intestine
2	chr12:57326400-57335200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:57327000-57335200	Weak transcription	Spleen	Spleen
4	chr12:57328200-57335000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:57329400-57335200	Weak transcription	A549	lung
6	chr12:57329800-57335000	Weak transcription	NHEK	skin
7	chr12:57330000-57334600	Weak transcription	HMEC	breast
8	chr12:57330000-57335200	Weak transcription	K562	blood
9	chr12:57330200-57335200	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links