Variant report

Variant	rs6780654
Chromosome Location	chr3:100244677-100244678
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10936221	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11719592	0.94[CHB][hapmap]
rs12634317	0.94[CHB][hapmap]
rs12636452	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs12639465	0.89[CHB][hapmap]
rs28722928	0.83[CHB][hapmap]
rs4073343	0.95[ASN][1000 genomes]
rs4075020	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes]
rs4077302	0.83[CHB][hapmap]
rs4928048	0.94[CHB][hapmap]
rs4928049	0.83[CHB][hapmap]
rs4928110	0.94[CHB][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4928111	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs4928112	0.94[CHB][hapmap]
rs55789829	0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs58689996	0.80[ASN][1000 genomes]
rs60272820	0.83[AFR][1000 genomes]
rs60511852	0.80[ASN][1000 genomes]
rs62276556	0.91[AFR][1000 genomes]
rs6441300	0.89[CHB][hapmap]
rs6441308	0.89[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6441316	0.94[CHB][hapmap]
rs6441328	0.94[CHB][hapmap]
rs6441329	0.94[CHB][hapmap]
rs6777810	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6792014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799879	0.94[CHB][hapmap]
rs6799882	0.94[CHB][hapmap]
rs6799992	0.94[CHB][hapmap]
rs6802787	0.94[CHB][hapmap]
rs6807804	0.94[CHB][hapmap]
rs6808426	0.94[CHB][hapmap]
rs7426815	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7429277	0.94[CHB][hapmap]
rs7429392	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap]
rs7431846	0.94[CHB][hapmap]
rs7433589	0.94[CHB][hapmap]
rs7611100	0.84[CHB][hapmap]
rs7622658	0.94[CHB][hapmap]
rs7631877	0.94[CHB][hapmap]
rs7645690	0.94[CHB][hapmap]
rs7645700	0.94[CHB][hapmap]
rs7647499	1.00[CHB][hapmap]
rs7653196	0.89[CHB][hapmap]
rs9809934	0.83[CHB][hapmap]
rs9819246	0.93[CHB][hapmap]
rs9823159	0.83[CHB][hapmap]
rs9843498	0.94[CHB][hapmap]
rs9855549	0.94[CHB][hapmap]
rs9865411	0.94[CHB][hapmap]
rs9865776	0.83[CHB][hapmap]
rs9880036	0.82[CHB][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	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100235800-100244800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:100238000-100252600	Weak transcription	Fetal Intestine Small	intestine
3	chr3:100238000-100265400	Weak transcription	HSMMtube	muscle
4	chr3:100239200-100244800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr3:100239400-100245000	Strong transcription	Fetal Stomach	stomach
6	chr3:100239400-100245200	Strong transcription	Aorta	Aorta
7	chr3:100241000-100299800	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:100241200-100251800	Weak transcription	Hela-S3	cervix
9	chr3:100241600-100244800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr3:100242000-100253200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:100242200-100246400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:100242400-100265000	Weak transcription	HepG2	liver
13	chr3:100242400-100268000	Weak transcription	Ovary	ovary
14	chr3:100243800-100245200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:100243800-100245600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:100243800-100246600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:100244000-100245000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:100244200-100245400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:100244400-100244800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:100244400-100244800	Enhancers	Esophagus	oesophagus
21	chr3:100244400-100244800	Enhancers	Placenta	Placenta
22	chr3:100244400-100244800	Enhancers	Pancreas	Pancrea
23	chr3:100244400-100244800	Enhancers	HSMM	muscle
24	chr3:100244400-100244800	Flanking Active TSS	NH-A	brain
25	chr3:100244400-100245200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:100244400-100245200	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr3:100244400-100245200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:100244400-100245400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:100244400-100245400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:100244400-100245400	Enhancers	Adipose Nuclei	Adipose
31	chr3:100244400-100245400	Flanking Active TSS	HMEC	breast
32	chr3:100244400-100245400	Flanking Active TSS	NHDF-Ad	bronchial
33	chr3:100244400-100245400	Flanking Active TSS	NHEK	skin
34	chr3:100244400-100245600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:100244400-100245800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:100244400-100247200	Enhancers	Liver	Liver
37	chr3:100244600-100244800	Flanking Active TSS	Rectal Smooth Muscle	rectum
38	chr3:100244600-100244800	Enhancers	Spleen	Spleen
39	chr3:100244600-100244800	Flanking Active TSS	Osteobl	bone
40	chr3:100244600-100245000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:100244600-100245000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:100244600-100245000	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr3:100244600-100245000	Enhancers	Fetal Heart	heart
44	chr3:100244600-100245000	Active TSS	Stomach Smooth Muscle	stomach
45	chr3:100244600-100245200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:100244600-100245200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:100244600-100245200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:100244600-100246400	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr3:100244600-100261400	Weak transcription	Fetal Lung	lung

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