Variant report

Variant	rs6794180
Chromosome Location	chr3:111530673-111530674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10934110	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10934116	0.86[CHD][hapmap]
rs11711475	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs11717092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12637888	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12695246	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4353782	0.85[ASN][1000 genomes]
rs4373041	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4472023	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4513422	0.91[EUR][1000 genomes]
rs4515020	0.85[ASN][1000 genomes]
rs4610200	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682063	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438015	0.92[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6438016	0.85[ASN][1000 genomes]
rs6438018	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6772828	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6772912	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6772930	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6783431	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs6809414	0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7620045	0.85[EUR][1000 genomes]
rs7634323	0.85[ASN][1000 genomes]
rs9288930	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs937554	0.80[TSI][hapmap]
rs9814037	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9816926	0.83[JPT][hapmap]
rs9817633	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9817777	0.92[CEU][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9829968	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9837252	0.84[ASN][1000 genomes]
rs9871340	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9876709	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]
rs9880495	0.83[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
rs6794180	PVRL3	cis	parietal	SCAN

Chromatin state (count:34 , 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	chr3:111522400-111531400	Weak transcription	Fetal Lung	lung
4	chr3:111526000-111531400	Enhancers	Hela-S3	cervix
5	chr3:111526400-111531000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:111526400-111531600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:111526400-111533000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr3:111526600-111531200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:111526600-111532200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:111526600-111532200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:111526600-111532200	Enhancers	NHEK	skin
12	chr3:111526600-111533000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:111526600-111533000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:111526800-111531400	Enhancers	HMEC	breast
15	chr3:111526800-111531800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:111526800-111531800	Enhancers	Osteobl	bone
17	chr3:111526800-111532000	Enhancers	NHDF-Ad	bronchial
18	chr3:111526800-111532200	Enhancers	HSMM	muscle
19	chr3:111526800-111532600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr3:111527000-111531200	Enhancers	NH-A	brain
21	chr3:111527000-111531600	Enhancers	HSMMtube	muscle
22	chr3:111527800-111532000	Enhancers	NHLF	lung
23	chr3:111528000-111531800	Enhancers	A549	lung
24	chr3:111528800-111531200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:111529000-111537800	Weak transcription	Liver	Liver
26	chr3:111529200-111531800	Weak transcription	Stomach Mucosa	stomach
27	chr3:111529400-111534600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:111529800-111531400	Enhancers	Colon Smooth Muscle	Colon
29	chr3:111529800-111532000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr3:111530000-111530800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:111530000-111531000	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr3:111530400-111532000	Enhancers	Fetal Kidney	kidney
33	chr3:111530600-111531000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:111530600-111532000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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