Variant report

Variant	rs7642942
Chromosome Location	chr3:100489286-100489287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11716316	0.81[JPT][hapmap]
rs12496951	0.90[CHD][hapmap]
rs13322026	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1354375	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs1394077	0.89[CHD][hapmap];0.89[ASN][1000 genomes]
rs1503839	0.90[CHD][hapmap]
rs1503845	0.90[CHD][hapmap]
rs16842822	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16842839	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16842845	0.90[CHD][hapmap]
rs3736534	0.92[CHD][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs544500	0.92[CHD][hapmap]
rs58758917	0.88[AFR][1000 genomes]
rs754462	0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs7609779	0.86[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7612334	0.80[JPT][hapmap]
rs7613610	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs7632038	0.86[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs764684	0.90[CHD][hapmap]
rs7648469	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7652511	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9290224	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs983474	0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs9842968	0.91[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs9850273	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs9860967	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9881972	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs989793	0.80[JPT][hapmap]
rs989795	0.90[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751972	chr3:100342493-100493062	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv432469	chr3:100342493-100493062	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
2	chr3:100467400-100497600	Weak transcription	Fetal Intestine Small	intestine
3	chr3:100469800-100498200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:100469800-100501400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:100470200-100498400	Weak transcription	Right Ventricle	heart
6	chr3:100471000-100495800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:100471600-100500400	Weak transcription	Lung	lung
8	chr3:100471800-100494600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:100471800-100502000	Weak transcription	Brain Anterior Caudate	brain
10	chr3:100472800-100494400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:100473800-100496400	Weak transcription	Fetal Intestine Large	intestine
12	chr3:100474400-100494200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:100474400-100500200	Weak transcription	HSMM	muscle
14	chr3:100474400-100501200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:100475000-100499000	Weak transcription	Placenta	Placenta
16	chr3:100475600-100520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:100478400-100496600	Weak transcription	Aorta	Aorta
18	chr3:100478800-100502000	Weak transcription	Psoas Muscle	Psoas
19	chr3:100479400-100493000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:100480200-100493800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:100486000-100489400	Weak transcription	Left Ventricle	heart
22	chr3:100487400-100490000	Strong transcription	Osteobl	bone
23	chr3:100487600-100489800	Strong transcription	NHDF-Ad	bronchial
24	chr3:100487600-100490000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr3:100487800-100489800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:100488000-100489600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:100488200-100489400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:100488200-100490000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr3:100488400-100490000	Strong transcription	Fetal Muscle Leg	muscle
30	chr3:100488600-100489800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:100488600-100489800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr3:100488600-100489800	Strong transcription	Fetal Stomach	stomach
33	chr3:100488600-100489800	Strong transcription	Ovary	ovary
34	chr3:100488600-100490000	Strong transcription	Colon Smooth Muscle	Colon
35	chr3:100488600-100490000	Strong transcription	HSMMtube	muscle
36	chr3:100488600-100504600	Weak transcription	Adipose Nuclei	Adipose
37	chr3:100488800-100489600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:100488800-100489600	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr3:100488800-100489800	Enhancers	H1 Cell Line	embryonic stem cell
40	chr3:100489000-100489400	Weak transcription	Gastric	stomach
41	chr3:100489000-100494400	Weak transcription	Fetal Lung	lung

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