Variant report

Variant	rs2666506
Chromosome Location	chr1:62740446-62740447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10493320	0.82[AMR][1000 genomes]
rs12063531	0.82[AMR][1000 genomes]
rs12078087	0.82[AMR][1000 genomes]
rs12079207	0.82[AMR][1000 genomes]
rs12718429	0.82[AMR][1000 genomes]
rs1555833	0.80[ASN][1000 genomes]
rs2258470	0.81[JPT][hapmap]
rs2666474	0.82[JPT][hapmap]
rs2666487	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666488	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666503	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2666507	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666508	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765247	0.82[JPT][hapmap]
rs2765249	0.81[JPT][hapmap]
rs2765250	0.82[ASN][1000 genomes]
rs2765251	1.00[CHB][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2765258	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34752481	0.88[AMR][1000 genomes]
rs7516290	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs912894	0.82[AMR][1000 genomes]
rs912895	0.82[AMR][1000 genomes]
rs912896	0.82[AMR][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:27 , 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	chr1:62733000-62741000	Weak transcription	Brain Germinal Matrix	brain
3	chr1:62734200-62750800	Weak transcription	Gastric	stomach
4	chr1:62735800-62740600	Strong transcription	Placenta Amnion	Placenta Amnion
5	chr1:62736400-62741000	Strong transcription	HepG2	liver
6	chr1:62737000-62740600	Genic enhancers	Fetal Muscle Trunk	muscle
7	chr1:62737600-62740600	Strong transcription	Fetal Intestine Small	intestine
8	chr1:62737600-62741800	Strong transcription	Placenta	Placenta
9	chr1:62737800-62742600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:62737800-62744400	Weak transcription	Fetal Intestine Large	intestine
11	chr1:62738000-62749000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:62738200-62746400	Weak transcription	Fetal Kidney	kidney
13	chr1:62738200-62751200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:62738400-62740600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:62738800-62740600	Genic enhancers	Fetal Muscle Leg	muscle
16	chr1:62739200-62740600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:62739400-62740800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:62739400-62740800	Genic enhancers	Fetal Stomach	stomach
19	chr1:62739600-62744200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:62740000-62741200	Enhancers	Fetal Heart	heart
21	chr1:62740200-62746400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:62740400-62740600	Genic enhancers	Adipose Nuclei	Adipose
23	chr1:62740400-62740600	Enhancers	Fetal Brain Male	brain
24	chr1:62740400-62743200	Weak transcription	Liver	Liver
25	chr1:62740400-62744600	Weak transcription	Fetal Thymus	thymus
26	chr1:62740400-62745400	Weak transcription	Fetal Lung	lung
27	chr1:62740400-62746600	Weak transcription	Pancreas	Pancrea

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