Variant report

Variant	rs12093484
Chromosome Location	chr1:85768860-85768861
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	chr1:85038431..85040264-chr1:85767538..85769464,2	K562	blood:
2	chr1:85763770..85765499-chr1:85767346..85769408,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117151	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10747317	0.90[CHB][hapmap]
rs10782542	0.90[CHB][hapmap]
rs10782543	0.90[CHB][hapmap]
rs11161573	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs11161585	0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[ASN][1000 genomes]
rs11161586	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11161588	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11161592	1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11576939	1.00[CHB][hapmap]
rs11583827	1.00[CHB][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11585614	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587512	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]
rs11590047	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12061305	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12405767	1.00[CHB][hapmap]
rs12754032	0.88[ASN][1000 genomes]
rs17125445	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012099	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34743622	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4949927	1.00[CHB][hapmap]
rs4949928	1.00[CHB][hapmap]
rs57483398	0.84[ASN][1000 genomes]
rs61771982	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6668948	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6670921	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs7554249	1.00[CHB][hapmap];0.87[GIH][hapmap];0.83[LWK][hapmap];0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12093484	GBP3	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
2	chr1:85764400-85769000	Weak transcription	Fetal Stomach	stomach
3	chr1:85764400-85774000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:85764800-85770400	Weak transcription	NHDF-Ad	bronchial
5	chr1:85765000-85769000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:85765200-85773600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:85765200-85773600	Weak transcription	HMEC	breast
8	chr1:85768000-85769800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:85768200-85773600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:85768200-85773600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:85768400-85769600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:85768400-85772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:85768400-85773400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:85768600-85769400	Enhancers	Fetal Muscle Leg	muscle
15	chr1:85768800-85769200	Enhancers	Adipose Nuclei	Adipose

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