Variant report

Variant	rs12040780
Chromosome Location	chr1:209879846-209879847
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10489341	0.82[CHB][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.84[MKK][hapmap]
rs11119333	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799643	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12024779	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12075595	1.00[EUR][1000 genomes]
rs17015053	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015095	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17015099	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs56679555	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56822893	0.91[AFR][1000 genomes]
rs57606822	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58627173	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61279558	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680324	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs846909	1.00[CHB][hapmap]
rs846911	1.00[CHB][hapmap]
rs846914	1.00[CHB][hapmap]
rs860185	1.00[CHB][hapmap]
rs861762	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1004343	chr1:209879304-209909385	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209870800-209880000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209870800-209880200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:209875200-209882400	Enhancers	Brain Substantia Nigra	brain
4	chr1:209877400-209882600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:209878400-209880800	Weak transcription	Brain Germinal Matrix	brain
6	chr1:209878400-209881800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:209878600-209881200	Weak transcription	Brain Anterior Caudate	brain
8	chr1:209878600-209881400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:209878600-209888200	Weak transcription	Brain Angular Gyrus	brain
10	chr1:209878800-209880400	Weak transcription	NHLF	lung
11	chr1:209878800-209893400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:209879000-209881400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:209879200-209880400	Flanking Active TSS	Liver	Liver
14	chr1:209879400-209880000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:209879400-209880800	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:209879400-209881000	Weak transcription	Adipose Nuclei	Adipose
17	chr1:209879600-209880600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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