Variant report

Variant	rs9405538
Chromosome Location	chr6:2009988-2009989
allele	A/C
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:14)

rs_ID	r²[population]
rs11242728	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12193559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12197569	1.00[AMR][1000 genomes]
rs12199891	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12200671	0.81[EUR][1000 genomes]
rs12200728	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12207776	1.00[AMR][1000 genomes]
rs12209238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12213464	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830120	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72830125	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72830127	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9391940	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv981098	chr6:2008599-2102267	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1985000-2010200	Weak transcription	Fetal Intestine Large	intestine
2	chr6:1990400-2010800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr6:1992800-2010200	Weak transcription	Fetal Intestine Small	intestine
4	chr6:1993000-2021200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:2000000-2021200	Weak transcription	Small Intestine	intestine
6	chr6:2006200-2034800	Weak transcription	HepG2	liver
7	chr6:2008200-2021200	Weak transcription	Left Ventricle	heart
8	chr6:2008800-2010400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:2008800-2011800	Weak transcription	Gastric	stomach
10	chr6:2008800-2012400	Weak transcription	Pancreas	Pancrea
11	chr6:2009000-2010200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:2009200-2011600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:2009600-2010800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr6:2009600-2021000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:2009800-2021000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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

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