Variant report

Variant	rs2666483
Chromosome Location	chr1:62745478-62745479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10889317	0.86[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs11207949	0.90[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12037540	0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs12044289	0.86[EUR][1000 genomes]
rs12082623	0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs12095173	0.90[JPT][hapmap]
rs1325742	0.81[CEU][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1886831	0.86[CEU][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs1886832	0.86[CEU][hapmap];0.85[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs2666501	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2666502	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3844054	0.86[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs3850631	0.85[EUR][1000 genomes]
rs3895339	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4915609	0.85[JPT][hapmap]
rs4915811	0.85[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs4915812	0.81[CEU][hapmap]
rs6587965	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6663943	0.80[ASW][hapmap];0.82[LWK][hapmap];0.85[EUR][1000 genomes]
rs7551135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62732400-62748400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:62734200-62750800	Weak transcription	Gastric	stomach
3	chr1:62738000-62749000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:62738200-62746400	Weak transcription	Fetal Kidney	kidney
5	chr1:62738200-62751200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:62740200-62746400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:62740400-62746600	Weak transcription	Pancreas	Pancrea
8	chr1:62743200-62746800	Weak transcription	HMEC	breast
9	chr1:62743200-62747800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:62743400-62746200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:62743400-62746600	Weak transcription	Fetal Intestine Small	intestine
12	chr1:62744000-62746400	Weak transcription	Liver	Liver
13	chr1:62744400-62745600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:62744400-62746200	Enhancers	Fetal Muscle Leg	muscle
15	chr1:62744400-62746400	Enhancers	Fetal Heart	heart
16	chr1:62744600-62745600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:62744600-62745600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:62744600-62745800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:62744600-62745800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:62744600-62745800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr1:62744600-62746000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:62744600-62746200	Enhancers	Fetal Muscle Trunk	muscle
23	chr1:62744600-62746200	Enhancers	Placenta	Placenta
24	chr1:62744800-62746200	Enhancers	Adipose Nuclei	Adipose
25	chr1:62744800-62746400	Enhancers	Fetal Stomach	stomach
26	chr1:62744800-62747600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:62744800-62750800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr1:62745000-62746400	Enhancers	HSMMtube	muscle
29	chr1:62745000-62747000	Strong transcription	HepG2	liver
30	chr1:62745200-62745600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
31	chr1:62745200-62745800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr1:62745400-62745600	Enhancers	Fetal Thymus	thymus
33	chr1:62745400-62745800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
34	chr1:62745400-62746000	Enhancers	Fetal Lung	lung
35	chr1:62745400-62746400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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