Variant report

Variant	rs1009099
Chromosome Location	chr6:49576008-49576009
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10080998	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1268282	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1268285	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1570064	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1977203	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2180722	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2246758	1.00[CEU][hapmap]
rs2518102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2753077	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs471198	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6458710	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458714	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6918385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6925215	0.94[EUR][1000 genomes]
rs6941167	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs802069	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9369912	0.94[AMR][1000 genomes];0.94[EUR][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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49572600-49586600	Strong transcription	K562	blood
2	chr6:49574400-49577000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr6:49574400-49577200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr6:49574400-49577400	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr6:49574400-49577400	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr6:49574600-49577200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:49574800-49576800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:49575000-49576200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:49575000-49576200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:49575400-49576800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:49575400-49576800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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

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