Variant report

Variant	rs11888377
Chromosome Location	chr2:56001849-56001850
allele	C/G/T
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:15)

rs_ID	r²[population]
rs10496051	0.80[EUR][1000 genomes]
rs10496052	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11125602	0.80[EUR][1000 genomes]
rs11893573	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1346794	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864457	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985163	0.80[EUR][1000 genomes]
rs2009262	0.82[EUR][1000 genomes]
rs59556444	0.82[EUR][1000 genomes]
rs62167688	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62167689	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62167713	0.82[EUR][1000 genomes]
rs6752931	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7590753	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7601401	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv999962	chr2:55976574-56011517	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv997683	chr2:55976574-56013875	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv431080	chr2:55988293-56011517	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 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	chr2:55989400-56015000	Weak transcription	Aorta	Aorta
2	chr2:55999800-56003000	Weak transcription	Stomach Mucosa	stomach
3	chr2:55999800-56003400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:56000000-56003400	Weak transcription	NHEK	skin
5	chr2:56000000-56003600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:56000000-56003600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:56000000-56003600	Weak transcription	HMEC	breast
8	chr2:56000000-56005000	Weak transcription	A549	lung
9	chr2:56000000-56005200	Weak transcription	Hela-S3	cervix
10	chr2:56000200-56002200	Weak transcription	HUVEC	blood vessel
11	chr2:56001800-56002000	Enhancers	Breast Myoepithelial Primary Cells	Breast

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links