Variant report

Variant	rs6680953
Chromosome Location	chr1:62699069-62699070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1050334	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789108	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10889309	0.99[ASN][1000 genomes]
rs10889310	0.87[ASN][1000 genomes]
rs10889312	0.86[AMR][1000 genomes]
rs10889313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10889315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11207941	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207942	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207943	0.99[ASN][1000 genomes]
rs11207944	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11207945	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207946	0.99[ASN][1000 genomes]
rs11207947	0.88[ASN][1000 genomes]
rs11207948	0.87[ASN][1000 genomes]
rs12030846	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12089897	0.99[ASN][1000 genomes]
rs12096118	0.86[ASN][1000 genomes]
rs12120789	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138777	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144282	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067994	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2457812	0.86[ASN][1000 genomes]
rs2481689	0.85[ASN][1000 genomes]
rs2666478	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2774928	0.99[ASN][1000 genomes]
rs41289438	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4322258	0.92[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs55673263	0.87[ASN][1000 genomes]
rs56318037	0.86[ASN][1000 genomes]
rs61775734	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61775736	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61775737	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660963	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6664672	0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6688986	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696307	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553446	1.00[CHB][hapmap];1.00[JPT][hapmap];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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62693600-62700800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:62693600-62700800	Enhancers	Placenta	Placenta
3	chr1:62694400-62699400	Enhancers	HMEC	breast
4	chr1:62695800-62703400	Weak transcription	Adipose Nuclei	Adipose
5	chr1:62696000-62700000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:62696000-62700200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:62696600-62703600	Weak transcription	Fetal Stomach	stomach
8	chr1:62697000-62699800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:62697000-62700200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:62697000-62702800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:62697000-62703600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:62697000-62706600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:62697200-62700400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:62697200-62702800	Weak transcription	A549	lung
15	chr1:62697400-62699800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:62697400-62700200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:62697400-62700400	Weak transcription	HSMM	muscle
18	chr1:62697400-62701800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:62697400-62702400	Weak transcription	NH-A	brain
20	chr1:62697400-62703200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:62697600-62699600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:62697600-62700000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:62698000-62701000	Enhancers	Placenta Amnion	Placenta Amnion
24	chr1:62698200-62699600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:62698200-62704000	Enhancers	NHEK	skin
26	chr1:62698400-62699200	Enhancers	Fetal Muscle Leg	muscle
27	chr1:62698600-62699800	Enhancers	HSMMtube	muscle
28	chr1:62698600-62700000	Enhancers	Fetal Muscle Trunk	muscle
29	chr1:62698600-62701000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:62698600-62701200	Enhancers	HepG2	liver
31	chr1:62698600-62704400	Enhancers	Hela-S3	cervix
32	chr1:62698800-62699200	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr1:62698800-62699200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:62698800-62701000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:62699000-62700200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:62699000-62702800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:62699000-62706600	Weak transcription	Fetal Lung	lung
38	chr1:62699000-62706800	Weak transcription	Pancreas	Pancrea

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