Variant report

Variant	rs4762700
Chromosome Location	chr12:21536131-21536132
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:21528193..21534017-chr12:21534075..21538760,6	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1056007	0.93[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11046005	0.80[AFR][1000 genomes]
rs11834359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs12300126	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12305367	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12306121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12308285	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12317073	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12319824	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12811082	0.93[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12826226	0.93[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12826421	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12833409	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs17680787	0.93[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34417126	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34996992	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4762821	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5484	0.93[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5488	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7137767	1.00[LWK][hapmap];0.81[MKK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs7304919	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964783	0.93[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv557735	chr12:21443282-21538957	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv469161	chr12:21507702-21555691	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv557737	chr12:21507702-21555691	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1040888	chr12:21522271-21568550	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv557739	chr12:21526472-21543215	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv519603	chr12:21526472-21584709	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv470274	chr12:21531437-21568050	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv469162	chr12:21532100-21568051	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv557740	chr12:21532100-21568051	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4762700	LST-3TM12	cis	cerebellum	SCAN
rs4762700	PYROXD1	cis	cerebellum	SCAN
rs4762700	PLEKHA5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21535800-21537400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links