Variant report

Variant	rs7553446
Chromosome Location	chr1:62711203-62711204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1050334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10789108	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10889309	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10889310	0.85[ASN][1000 genomes]
rs10889313	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11207941	0.99[ASN][1000 genomes]
rs11207942	0.92[ASN][1000 genomes]
rs11207943	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207944	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11207946	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207947	0.87[ASN][1000 genomes]
rs11207948	0.86[ASN][1000 genomes]
rs12030846	0.92[ASN][1000 genomes]
rs12089897	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12096118	0.84[ASN][1000 genomes]
rs12120789	0.99[ASN][1000 genomes]
rs12138777	0.95[ASN][1000 genomes]
rs12144282	0.99[ASN][1000 genomes]
rs2067994	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457812	0.87[ASN][1000 genomes]
rs2481689	0.83[ASN][1000 genomes]
rs2666478	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2774928	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs41289438	0.99[ASN][1000 genomes]
rs4322258	0.90[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs55673263	0.86[ASN][1000 genomes]
rs56318037	0.85[ASN][1000 genomes]
rs61775734	0.99[ASN][1000 genomes]
rs61775736	0.99[ASN][1000 genomes]
rs61775737	0.99[ASN][1000 genomes]
rs6660963	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664672	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6680953	0.99[ASN][1000 genomes]
rs6688986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6696307	1.00[ASN][1000 genomes]
rs6696486	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62704000-62711400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:62704000-62720600	Weak transcription	Right Atrium	heart
3	chr1:62704200-62711600	Weak transcription	Adipose Nuclei	Adipose
4	chr1:62704200-62712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:62704400-62713200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:62706400-62713200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:62707600-62719600	Weak transcription	Fetal Kidney	kidney
8	chr1:62707600-62732000	Weak transcription	Gastric	stomach
9	chr1:62707800-62711800	Weak transcription	Esophagus	oesophagus
10	chr1:62707800-62712000	Weak transcription	Colonic Mucosa	Colon
11	chr1:62707800-62713200	Weak transcription	Fetal Brain Female	brain
12	chr1:62707800-62727400	Weak transcription	Pancreas	Pancrea
13	chr1:62708000-62713000	Weak transcription	Fetal Heart	heart
14	chr1:62708200-62720000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:62710000-62712000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:62710400-62711400	Enhancers	HepG2	liver
17	chr1:62710400-62712000	Strong transcription	Placenta	Placenta
18	chr1:62710400-62713600	Strong transcription	Fetal Stomach	stomach
19	chr1:62710600-62711400	Enhancers	HMEC	breast
20	chr1:62710600-62711400	Enhancers	NHEK	skin
21	chr1:62710600-62711600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:62710600-62711800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:62710600-62713800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr1:62710600-62713800	Strong transcription	Fetal Muscle Leg	muscle
25	chr1:62710800-62711400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:62710800-62711600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:62710800-62712000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:62710800-62731800	Weak transcription	Fetal Intestine Small	intestine
29	chr1:62711000-62711400	Weak transcription	Fetal Lung	lung
30	chr1:62711200-62711800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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