Variant report

Variant	rs9876709
Chromosome Location	chr3:111528539-111528540
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	chr3:111521862..111524115-chr3:111526095..111528698,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10934110	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10934114	0.83[TSI][hapmap]
rs11717092	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[EUR][1000 genomes]
rs12637888	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3925081	0.83[TSI][hapmap]
rs4373041	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4472023	0.96[CEU][hapmap];0.83[CHB][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4513422	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4610200	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs4682063	0.93[EUR][1000 genomes]
rs6438015	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6438018	0.97[EUR][1000 genomes]
rs6772828	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6772912	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6772930	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6783431	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6794180	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7620045	0.88[EUR][1000 genomes]
rs9288930	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs937554	0.85[TSI][hapmap]
rs9814037	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs9817633	0.81[EUR][1000 genomes]
rs9817777	0.92[CEU][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9829968	0.97[EUR][1000 genomes]
rs9871340	0.87[EUR][1000 genomes]
rs9880495	0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9876709	PVRL3	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111514600-111533200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:111521200-111531000	Weak transcription	Small Intestine	intestine
3	chr3:111522000-111528600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:111522400-111531400	Weak transcription	Fetal Lung	lung
5	chr3:111525800-111529000	Enhancers	Fetal Intestine Small	intestine
6	chr3:111526000-111531400	Enhancers	Hela-S3	cervix
7	chr3:111526200-111529000	Enhancers	Liver	Liver
8	chr3:111526400-111529000	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr3:111526400-111529400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:111526400-111529400	Enhancers	Pancreas	Pancrea
11	chr3:111526400-111531000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:111526400-111531600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:111526400-111533000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr3:111526600-111531200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:111526600-111532200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:111526600-111532200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:111526600-111532200	Enhancers	NHEK	skin
18	chr3:111526600-111533000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:111526600-111533000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:111526800-111528600	Enhancers	Colon Smooth Muscle	Colon
21	chr3:111526800-111529000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:111526800-111531400	Enhancers	HMEC	breast
23	chr3:111526800-111531800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:111526800-111531800	Enhancers	Osteobl	bone
25	chr3:111526800-111532000	Enhancers	NHDF-Ad	bronchial
26	chr3:111526800-111532200	Enhancers	HSMM	muscle
27	chr3:111526800-111532600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr3:111527000-111529000	Enhancers	Fetal Kidney	kidney
29	chr3:111527000-111531200	Enhancers	NH-A	brain
30	chr3:111527000-111531600	Enhancers	HSMMtube	muscle
31	chr3:111527200-111528600	Weak transcription	Aorta	Aorta
32	chr3:111527200-111529400	Enhancers	HepG2	liver
33	chr3:111527200-111530000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:111527400-111529200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:111527800-111529000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:111527800-111529200	Enhancers	Stomach Mucosa	stomach
37	chr3:111527800-111530000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:111527800-111532000	Enhancers	NHLF	lung
39	chr3:111528000-111531800	Enhancers	A549	lung
40	chr3:111528200-111528600	Enhancers	Rectal Smooth Muscle	rectum
41	chr3:111528400-111528600	Enhancers	Fetal Intestine Large	intestine
42	chr3:111528400-111529800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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