Variant report

Variant	rs2039553
Chromosome Location	chr13:80299722-80299723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1335293	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414116	0.83[EUR][1000 genomes]
rs1577404	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2039552	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2095470	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2329119	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2329120	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4591027	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7139876	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8001312	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9530951	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9545179	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9565521	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9574460	0.93[AMR][1000 genomes];0.87[EUR][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	nsv900588	chr13:80216846-80421340	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv900589	chr13:80250511-80310295	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1039333	chr13:80289936-80333167	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Pancreatic cancer	20686608	GWAS catalog

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80296600-80300600	Enhancers	HSMM	muscle
2	chr13:80296600-80301400	Enhancers	Fetal Intestine Small	intestine
3	chr13:80296600-80301600	Enhancers	Fetal Intestine Large	intestine
4	chr13:80296800-80300000	Enhancers	Fetal Heart	heart
5	chr13:80296800-80300400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr13:80297200-80300800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr13:80297400-80300200	Enhancers	Duodenum Mucosa	Duodenum
8	chr13:80297600-80300400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:80298000-80300600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr13:80298000-80300600	Enhancers	Fetal Lung	lung
11	chr13:80298200-80302200	Enhancers	HSMMtube	muscle
12	chr13:80299200-80300000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr13:80299200-80300000	Enhancers	HUVEC	blood vessel
14	chr13:80299400-80300400	Enhancers	A549	lung
15	chr13:80299400-80301400	Enhancers	Fetal Muscle Leg	muscle
16	chr13:80299400-80310000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr13:80299600-80300200	Weak transcription	Fetal Stomach	stomach
18	chr13:80299600-80300400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr13:80299600-80300400	Enhancers	Small Intestine	intestine

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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

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