Variant report

Variant	rs2089735
Chromosome Location	chr3:156342552-156342553
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156271473..156272989-chr3:156341064..156343345,2	MCF-7	breast:
2	chr3:156324594..156326430-chr3:156340933..156343753,2	K562	blood:
3	chr3:156342470..156344204-chr3:156404618..156406838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114850	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11711144	0.99[ASN][1000 genomes]
rs12489699	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493167	0.83[AMR][1000 genomes]
rs12631936	0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs12696038	0.86[CEU][hapmap]
rs13090418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13314546	0.86[CEU][hapmap]
rs16826570	0.86[CEU][hapmap]
rs16826572	0.86[CEU][hapmap]
rs17367831	0.86[CEU][hapmap]
rs2102506	0.93[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2320895	0.84[CEU][hapmap]
rs6441080	0.86[CEU][hapmap]
rs6650896	0.86[CEU][hapmap]
rs6762513	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6762762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6807235	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808027	0.86[CEU][hapmap]
rs7618375	0.86[CEU][hapmap]
rs7632294	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7640295	0.85[CEU][hapmap]
rs7640363	0.86[CEU][hapmap]
rs7652356	0.86[CEU][hapmap]
rs874641	0.86[CEU][hapmap]
rs874642	0.83[CEU][hapmap]
rs874662	0.86[CEU][hapmap]
rs9811767	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs9819659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9831507	0.86[CEU][hapmap]
rs9832367	0.85[CEU][hapmap]
rs9833654	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9843340	0.86[CEU][hapmap]
rs9865431	0.93[CEU][hapmap]
rs9870053	0.85[CEU][hapmap]
rs9870256	0.86[CEU][hapmap]
rs9870575	0.85[CEU][hapmap]
rs9882596	0.86[CEU][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	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
2	nsv829764	chr3:156174824-156347774	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	nsv877684	chr3:156294987-156344825	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2089735	GMPS	cis	parietal	SCAN
rs2089735		cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156336400-156345800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:156338400-156343400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:156338800-156343600	Weak transcription	Fetal Intestine Large	intestine
4	chr3:156338800-156345800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:156339000-156343400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:156339000-156343600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:156339000-156343800	Weak transcription	K562	blood
8	chr3:156339200-156343600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:156339200-156343600	Weak transcription	HMEC	breast
10	chr3:156339200-156343600	Weak transcription	NHEK	skin
11	chr3:156339200-156343800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:156339200-156346000	Weak transcription	HSMM	muscle
13	chr3:156339200-156347800	Weak transcription	Esophagus	oesophagus
14	chr3:156339600-156343400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:156341200-156343600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:156342000-156342800	Weak transcription	Lung	lung
17	chr3:156342200-156345000	Weak transcription	Fetal Heart	heart

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