Variant report

Variant	rs11161585
Chromosome Location	chr1:85761663-85761664
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:85740595..85746052-chr1:85759606..85765261,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142867	Chromatin interaction
ENSG00000223653	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	0.80[CHB][hapmap]
rs10782542	0.80[CHB][hapmap]
rs10782543	0.80[CHB][hapmap]
rs11161573	0.89[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs11161586	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161588	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161592	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11576939	0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11580090	0.86[ASN][1000 genomes]
rs11583827	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585614	0.88[ASN][1000 genomes]
rs11587512	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]
rs11590047	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12061305	0.87[ASN][1000 genomes]
rs12061512	0.85[ASN][1000 genomes]
rs12093484	0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[ASN][1000 genomes]
rs12405767	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12754032	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17125445	0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[ASN][1000 genomes]
rs2012099	0.84[ASN][1000 genomes]
rs34743622	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949927	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs4949928	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs57483398	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60325409	0.83[ASN][1000 genomes]
rs61771982	0.89[ASN][1000 genomes]
rs6668948	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670921	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.98[ASN][1000 genomes]
rs7554249	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9432848	0.80[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
rs11161585	C1orf52	cis	cerebellum	SCAN
rs11161585	GBP3	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85742800-85763000	Weak transcription	Ovary	ovary
2	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
3	chr1:85748600-85764000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:85750000-85762800	Weak transcription	Pancreas	Pancrea
5	chr1:85750400-85762800	Weak transcription	Fetal Intestine Small	intestine
6	chr1:85750800-85763800	Weak transcription	Primary B cells from cord blood	blood
7	chr1:85752200-85762800	Weak transcription	Aorta	Aorta
8	chr1:85755800-85763200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:85756000-85762800	Enhancers	NHEK	skin
10	chr1:85756400-85762600	Weak transcription	Stomach Mucosa	stomach
11	chr1:85756600-85763200	Weak transcription	GM12878-XiMat	blood
12	chr1:85757000-85762800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:85757800-85762400	Weak transcription	HSMM	muscle
14	chr1:85757800-85762600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:85758600-85763000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:85759000-85763000	Enhancers	HMEC	breast
17	chr1:85759200-85763400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:85759600-85765200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:85759800-85763200	Enhancers	NHLF	lung
20	chr1:85759800-85763400	Enhancers	HUVEC	blood vessel
21	chr1:85760400-85763000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:85760600-85761800	Enhancers	Fetal Stomach	stomach
23	chr1:85760600-85762800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:85760800-85761800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:85761000-85761800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr1:85761000-85762800	Weak transcription	HSMMtube	muscle
27	chr1:85761200-85761800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:85761200-85761800	Enhancers	Spleen	Spleen
29	chr1:85761200-85762400	Weak transcription	Osteobl	bone
30	chr1:85761400-85761800	Enhancers	Esophagus	oesophagus
31	chr1:85761400-85761800	Enhancers	Lung	lung
32	chr1:85761400-85762400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:85761400-85762600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:85761400-85762600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:85761400-85762600	Weak transcription	Fetal Lung	lung
36	chr1:85761400-85762800	Weak transcription	Fetal Intestine Large	intestine
37	chr1:85761600-85762600	Weak transcription	NH-A	brain
38	chr1:85761600-85762600	Weak transcription	NHDF-Ad	bronchial
39	chr1:85761600-85762800	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:85761600-85763000	Weak transcription	Adipose Nuclei	Adipose

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