Variant report

Variant	rs9840340
Chromosome Location	chr3:111516317-111516318
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	chr20:55698433..55700361-chr3:111514654..111517522,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12635594	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072118	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56400016	0.93[ASN][1000 genomes]
rs6438013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6438014	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs9811721	0.92[CEU][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs9857303	0.83[TSI][hapmap]

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

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111487800-111521000	Weak transcription	Gastric	stomach
2	chr3:111499000-111518800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:111501600-111518800	Weak transcription	A549	lung
4	chr3:111504000-111519000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:111505400-111520600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:111509400-111518800	Weak transcription	HepG2	liver
7	chr3:111509400-111525800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:111510200-111522000	Weak transcription	Left Ventricle	heart
9	chr3:111512200-111517600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:111513200-111517000	Enhancers	NHDF-Ad	bronchial
11	chr3:111513200-111521000	Weak transcription	Lung	lung
12	chr3:111513400-111517000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:111513800-111521000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:111514400-111518800	Weak transcription	Liver	Liver
15	chr3:111514600-111521000	Weak transcription	Fetal Stomach	stomach
16	chr3:111514600-111533200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:111514800-111518800	Weak transcription	Pancreas	Pancrea
18	chr3:111515200-111516400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:111515400-111516600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:111515400-111516800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:111515400-111517000	Enhancers	Adipose Nuclei	Adipose
22	chr3:111515800-111516800	Enhancers	Fetal Lung	lung
23	chr3:111515800-111520000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:111516000-111519400	Weak transcription	Osteobl	bone
25	chr3:111516000-111519600	Weak transcription	Colon Smooth Muscle	Colon

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