Variant report

Variant	rs10880664
Chromosome Location	chr12:45141654-45141655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11182546	1.00[CHB][hapmap]
rs11182547	1.00[CHB][hapmap]
rs11182553	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182555	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182558	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182566	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182568	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11182570	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182571	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182574	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182575	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11182576	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182587	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182593	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11182594	0.82[CHB][hapmap]
rs11182600	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182602	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182605	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182606	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182609	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182610	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11182611	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182613	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182614	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182615	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182616	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11182619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11182620	0.90[ASN][1000 genomes]
rs11182623	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11182624	1.00[ASN][1000 genomes]
rs11182625	0.95[ASN][1000 genomes]
rs11182626	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs11182628	0.80[ASN][1000 genomes]
rs11182629	1.00[ASN][1000 genomes]
rs11182632	1.00[ASN][1000 genomes]
rs11182637	0.95[ASN][1000 genomes]
rs11182638	0.95[ASN][1000 genomes]
rs11182641	0.85[ASN][1000 genomes]
rs11182642	0.85[ASN][1000 genomes]
rs11182643	0.95[ASN][1000 genomes]
rs11182644	0.95[ASN][1000 genomes]
rs11182645	0.95[ASN][1000 genomes]
rs11182646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11182648	0.95[ASN][1000 genomes]
rs11182649	0.95[ASN][1000 genomes]
rs11182650	0.85[ASN][1000 genomes]
rs11182651	0.95[ASN][1000 genomes]
rs11182652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11182653	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12227198	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12227809	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12228891	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12229463	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1452886	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17094988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6582510	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6582511	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7961698	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832394	chr12:45077573-45269305	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
3	nsv1049080	chr12:45097564-45195295	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv1036926	chr12:45131884-45273648	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv541484	chr12:45131884-45273648	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45123400-45142400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:45134400-45143400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:45134400-45165200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr12:45135400-45175000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:45139000-45142800	Weak transcription	Fetal Brain Female	brain
6	chr12:45141200-45142000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:45141400-45142000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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