Variant report

Variant	rs2486280
Chromosome Location	chr15:45751889-45751890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1153835	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1153845	0.81[ASN][1000 genomes]
rs1547487	0.80[ASN][1000 genomes]
rs2433616	0.80[ASN][1000 genomes]
rs55673230	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak 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 miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1523	chr15:45749900-45783825	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2486280	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs2486280	CTD-2651B20.4	cis	Artery Tibial	GTEx
rs2486280	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs2486280	CTD-2651B20.3	cis	lung	GTEx
rs2486280	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs2486280	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs2486280	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs2486280	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs2486280	CTD-2651B20.3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45749200-45753200	Weak transcription	Gastric	stomach
2	chr15:45749400-45753200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:45749400-45753200	Weak transcription	Esophagus	oesophagus
4	chr15:45749400-45753200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:45749800-45753800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:45750600-45753200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:45750600-45753600	Weak transcription	Pancreas	Pancrea
8	chr15:45750800-45781000	Weak transcription	Stomach Mucosa	stomach
9	chr15:45751200-45753200	Weak transcription	Colonic Mucosa	Colon
10	chr15:45751200-45753200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:45751200-45760000	Weak transcription	Fetal Stomach	stomach
12	chr15:45751200-45761200	Weak transcription	Fetal Intestine Small	intestine
13	chr15:45751200-45801600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:45751400-45753600	Weak transcription	Fetal Kidney	kidney
15	chr15:45751600-45752800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr15:45751600-45753400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:45751600-45753600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:45751800-45752000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell

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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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