Variant report

Variant	rs2777920
Chromosome Location	chr1:179776841-179776842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1148824	0.92[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1148825	0.89[GIH][hapmap];0.81[MEX][hapmap]
rs1281421	0.86[GIH][hapmap];0.81[MEX][hapmap]
rs1281422	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236589	0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2647226	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2794586	0.84[GIH][hapmap]
rs2794588	0.81[CEU][hapmap]
rs2794589	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3845386	0.84[CEU][hapmap];0.84[GIH][hapmap]
rs4320747	0.84[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6425594	0.88[CEU][hapmap];0.81[GIH][hapmap]
rs6658638	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6684425	0.92[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6690639	0.84[CEU][hapmap]
rs6695329	0.88[CEU][hapmap]
rs7552673	0.87[ASN][1000 genomes]
rs904272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[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	nsv1009961	chr1:179714247-179790110	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1011407	chr1:179733193-179799430	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv520418	chr1:179761601-179794602	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv519307	chr1:179766086-179795505	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179774600-179779600	Enhancers	Placenta	Placenta
2	chr1:179775200-179777000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:179776000-179778200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:179776200-179778200	Enhancers	Fetal Intestine Large	intestine
5	chr1:179776200-179779000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:179776200-179779200	Enhancers	Fetal Intestine Small	intestine
7	chr1:179776400-179778000	Enhancers	Osteobl	bone
8	chr1:179776600-179777200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:179776600-179778000	Enhancers	NH-A	brain
10	chr1:179776600-179778800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:179776600-179778800	Weak transcription	Esophagus	oesophagus
12	chr1:179776800-179777000	Weak transcription	Right Atrium	heart
13	chr1:179776800-179777200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:179776800-179777400	Enhancers	Duodenum Mucosa	Duodenum

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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