Variant report

Variant	rs12499206
Chromosome Location	chr4:87499237-87499238
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10000891	1.00[JPT][hapmap]
rs10001010	1.00[JPT][hapmap]
rs10001986	1.00[JPT][hapmap]
rs10003989	1.00[JPT][hapmap]
rs10020590	1.00[JPT][hapmap]
rs10023163	1.00[JPT][hapmap]
rs10024860	1.00[JPT][hapmap]
rs10028550	1.00[JPT][hapmap]
rs10029565	1.00[JPT][hapmap]
rs10033029	1.00[JPT][hapmap]
rs10033679	1.00[JPT][hapmap]
rs10470933	1.00[JPT][hapmap]
rs10516780	1.00[JPT][hapmap]
rs11097118	1.00[JPT][hapmap]
rs11097119	1.00[JPT][hapmap]
rs11938022	1.00[ASN][1000 genomes]
rs11947245	1.00[ASN][1000 genomes]
rs12498653	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12498681	1.00[JPT][hapmap]
rs12499471	1.00[JPT][hapmap]
rs12499575	1.00[JPT][hapmap]
rs12500797	1.00[JPT][hapmap]
rs12502487	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12502645	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12505291	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12505402	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12507034	1.00[JPT][hapmap]
rs12508156	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12508339	1.00[JPT][hapmap]
rs12508545	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12508579	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12508626	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12508746	1.00[JPT][hapmap]
rs12509039	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12509049	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12509430	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12509560	1.00[JPT][hapmap]
rs12510314	1.00[ASN][1000 genomes]
rs12510393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12512524	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12512858	1.00[JPT][hapmap]
rs13111757	1.00[JPT][hapmap]
rs13112139	1.00[JPT][hapmap]
rs13136651	1.00[JPT][hapmap]
rs13150561	1.00[JPT][hapmap]
rs1420620	1.00[JPT][hapmap]
rs17454432	1.00[JPT][hapmap]
rs17454655	1.00[JPT][hapmap]
rs4472106	1.00[ASN][1000 genomes]
rs7664147	1.00[JPT][hapmap]
rs7664860	1.00[JPT][hapmap]
rs7698481	1.00[JPT][hapmap]
rs7699564	1.00[JPT][hapmap]
rs9997453	1.00[JPT][hapmap]

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	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv879522	chr4:87473776-87644842	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv822635	chr4:87479576-87622176	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87480600-87502000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:87480800-87501800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:87492200-87499400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:87493800-87507000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:87496600-87512600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:87498800-87508600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:87499000-87502200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:87499200-87499600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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