Variant report

Variant	rs11587512
Chromosome Location	chr1:85765798-85765799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85764436..85767299-chr1:86046418..86049258,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10747317	0.90[CHB][hapmap]
rs10782542	0.90[CHB][hapmap]
rs10782543	0.90[CHB][hapmap]
rs11161573	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs11161585	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11576939	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11580090	0.86[ASN][1000 genomes]
rs11583827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585614	0.88[ASN][1000 genomes]
rs11590047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12061305	0.87[ASN][1000 genomes]
rs12061512	0.85[ASN][1000 genomes]
rs12093484	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12405767	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12754032	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125445	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.88[ASN][1000 genomes]
rs2012099	0.84[ASN][1000 genomes]
rs34743622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949927	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4949928	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs57483398	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60325409	0.83[ASN][1000 genomes]
rs61771982	0.89[ASN][1000 genomes]
rs6668948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670921	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7554249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9432848	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11587512	DDAH1	cis	cerebellum	SCAN
rs11587512	GBP3	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
2	chr1:85764200-85768400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:85764400-85768000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:85764400-85769000	Weak transcription	Fetal Stomach	stomach
5	chr1:85764400-85774000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:85764800-85766200	Weak transcription	Fetal Intestine Small	intestine
7	chr1:85764800-85768800	Weak transcription	Adipose Nuclei	Adipose
8	chr1:85764800-85770400	Weak transcription	NHDF-Ad	bronchial
9	chr1:85765000-85767000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:85765000-85768200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:85765000-85769000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:85765200-85773600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:85765200-85773600	Weak transcription	HMEC	breast
14	chr1:85765400-85767800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:85765600-85768000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:85765600-85768000	Weak transcription	Lung	lung

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