Variant report

Variant	rs6130040
Chromosome Location	chr20:40747812-40747813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12625871	0.80[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs16986553	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2223422	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs6029997	0.83[EUR][1000 genomes]
rs6093610	1.00[CEU][hapmap]
rs6124418	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6124419	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6124420	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6130039	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6130051	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6130052	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6130055	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8183826	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[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	nsv3381	chr20:39925326-40765696	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40715800-40757600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:40747000-40748600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr20:40747200-40748000	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr20:40747200-40758400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr20:40747400-40748400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr20:40747400-40751000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr20:40747800-40762400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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