Variant report

Variant	rs839091
Chromosome Location	chr12:86490553-86490554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10746359	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10779224	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10779225	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10779227	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10779236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10863128	0.87[ASN][1000 genomes]
rs10863129	0.82[EUR][1000 genomes]
rs10863139	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs10863141	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs10863149	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10863164	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11117148	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs11117152	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs11117154	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11513955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11614214	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12298516	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1354258	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1493407	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1502803	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs1698754	0.84[CEU][hapmap]
rs1847206	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61931120	0.87[ASN][1000 genomes]
rs61931121	0.87[ASN][1000 genomes]
rs61931135	0.83[ASN][1000 genomes]
rs6539944	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6539947	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136221	0.88[CEU][hapmap];0.87[ASN][1000 genomes]
rs7294859	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7295033	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7302043	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7307686	0.87[ASN][1000 genomes]
rs7398950	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7485853	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs7486591	0.95[CEU][hapmap]
rs7489114	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7961367	0.92[CEU][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7965726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967417	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7971447	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs839135	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs839139	1.00[YRI][hapmap]
rs839181	0.84[ASN][1000 genomes]
rs9669353	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9706029	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs9738989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9804820	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv832476	chr12:86389751-86497122	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3345033	chr12:86458294-86514745	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv470311	chr12:86484366-86550783	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86489800-86491400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:86490400-86491000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr12:86490400-86491400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr12:86490400-86491600	Enhancers	HUES48 Cell Line	embryonic stem cell

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