Variant report

Variant	rs2172836
Chromosome Location	chr15:38994113-38994114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17654449	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2036048	0.82[YRI][hapmap]
rs2643220	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2172836	C15orf54	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38988600-38994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:38989000-38997400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:38989000-38997600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:38989000-38997600	Weak transcription	HSMM	muscle
5	chr15:38991400-38996200	Weak transcription	Thymus	Thymus
6	chr15:38991800-38996400	Weak transcription	Fetal Thymus	thymus
7	chr15:38992200-38995400	Enhancers	Fetal Intestine Large	intestine
8	chr15:38992400-38995400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr15:38992800-38996800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr15:38993000-38995000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:38993000-38997600	Weak transcription	Small Intestine	intestine
12	chr15:38993200-38995400	Enhancers	Fetal Intestine Small	intestine
13	chr15:38993600-38994200	Enhancers	Duodenum Mucosa	Duodenum
14	chr15:38993600-38995200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:38993600-38995400	Enhancers	Pancreas	Pancrea
16	chr15:38993600-38995400	Enhancers	Stomach Mucosa	stomach
17	chr15:38994000-38994600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:38994000-38994600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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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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