Variant report

Variant	rs12058486
Chromosome Location	chr1:62767265-62767266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10493320	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207957	0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs12063531	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12078087	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12079207	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082238	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12085325	0.95[ASN][1000 genomes]
rs12718429	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724349	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12760895	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296518	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477872	0.94[ASN][1000 genomes]
rs2666487	0.94[ASN][1000 genomes]
rs2666488	0.94[ASN][1000 genomes]
rs2765258	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs2765261	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs2765263	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs34752481	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7520614	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs765691	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs765692	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs912894	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912895	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912896	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3320078	chr1:62765222-62770871	Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
6	esv3320079	chr1:62765252-62770865	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
7	esv3320077	chr1:62765307-62770822	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	inside rSNPs	diseases
8	esv3320080	chr1:62765307-62770822	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
9	nsv520333	chr1:62766527-62769887	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62754400-62773400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:62759800-62770800	Enhancers	Fetal Muscle Leg	muscle
3	chr1:62762200-62773200	Weak transcription	Fetal Lung	lung
4	chr1:62764800-62768000	Enhancers	Pancreas	Pancrea
5	chr1:62765000-62767600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:62765000-62768000	Enhancers	Fetal Stomach	stomach
7	chr1:62765200-62767600	Genic enhancers	HepG2	liver
8	chr1:62765600-62767800	Enhancers	Brain Substantia Nigra	brain
9	chr1:62766000-62768600	Weak transcription	Adipose Nuclei	Adipose
10	chr1:62766000-62770000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:62766000-62770200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:62766200-62767800	Weak transcription	Fetal Heart	heart
13	chr1:62766400-62767600	Weak transcription	Fetal Kidney	kidney
14	chr1:62766800-62768000	Enhancers	H9 Cell Line	embryonic stem cell
15	chr1:62766800-62770200	Weak transcription	Gastric	stomach
16	chr1:62767000-62767600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr1:62767000-62768000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:62767000-62769000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:62767200-62767400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
20	chr1:62767200-62767600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr1:62767200-62767600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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