Variant report

Variant	rs6684425
Chromosome Location	chr1:179763269-179763270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1148824	0.84[CEU][hapmap]
rs1281422	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236589	0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2647226	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2777920	0.92[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2794588	0.85[CEU][hapmap]
rs2794589	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3845386	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4320747	0.92[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6425594	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs6658638	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6690639	0.92[CEU][hapmap]
rs6695329	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs6701652	0.84[CEU][hapmap]
rs7552673	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs904272	0.92[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[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	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

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179757800-179764400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:179761800-179763400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:179762800-179764200	Enhancers	Left Ventricle	heart
4	chr1:179762800-179764600	Enhancers	HSMMtube	muscle
5	chr1:179762800-179765600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:179763000-179764400	Enhancers	Right Atrium	heart
7	chr1:179763200-179764600	Enhancers	Fetal Heart	heart
8	chr1:179763200-179764600	Enhancers	Fetal Intestine Large	intestine
9	chr1:179763200-179764600	Weak transcription	Pancreas	Pancrea
10	chr1:179763200-179764800	Enhancers	Fetal Intestine Small	intestine

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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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