Variant report

Variant	rs6690639
Chromosome Location	chr1:179761869-179761870
allele	A/G
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	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1148825	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1281420	0.82[ASN][1000 genomes]
rs1281421	0.81[CEU][hapmap]
rs2647225	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2777920	0.84[CEU][hapmap]
rs2794586	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2794588	1.00[JPT][hapmap]
rs3845386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4320747	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6425594	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6684425	0.92[CEU][hapmap]
rs6695329	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6701652	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7552673	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs904272	0.85[CEU][hapmap]

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:5 , 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	chr1:179761000-179762000	Enhancers	Fetal Intestine Small	intestine
3	chr1:179761400-179762800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:179761600-179763200	Weak transcription	Fetal Intestine Large	intestine
5	chr1:179761800-179763400	Weak transcription	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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