Variant report

Variant	rs12199891
Chromosome Location	chr6:2012489-2012490
allele	C/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: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]
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]
rs9405538	1.00[AMR][1000 genomes];1.00[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:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1993000-2021200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:2000000-2021200	Weak transcription	Small Intestine	intestine
3	chr6:2006200-2034800	Weak transcription	HepG2	liver
4	chr6:2008200-2021200	Weak transcription	Left Ventricle	heart
5	chr6:2009600-2021000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:2009800-2021000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:2011000-2021200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:2011400-2012800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr6:2012000-2013200	Weak transcription	Gastric	stomach

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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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