Variant report

Variant	rs2456526
Chromosome Location	chr15:53089442-53089443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10518694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2120450	0.88[EUR][1000 genomes]
rs2243790	0.89[CEU][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs2440317	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2440322	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2440376	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs2456507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2456522	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2456524	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2456525	0.96[EUR][1000 genomes]
rs2456529	0.93[EUR][1000 genomes]
rs2456530	0.89[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs2456532	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs28475375	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60065065	0.97[EUR][1000 genomes]
rs7180600	0.86[EUR][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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv457142	chr15:53041887-53091896	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	nsv569427	chr15:53041887-53091896	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
5	nsv1046970	chr15:53065114-53142386	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
6	nsv569428	chr15:53069874-53140045	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2456526	ORMDL3	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53087400-53090200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
2	chr15:53087600-53089800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
3	chr15:53087600-53091400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:53087800-53090200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
5	chr15:53088000-53089800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
6	chr15:53088200-53090200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:53088400-53090200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
8	chr15:53088600-53089800	Enhancers	Liver	Liver
9	chr15:53088800-53090200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:53089000-53090000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
11	chr15:53089200-53089800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:53089200-53090800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
13	chr15:53089400-53089600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
14	chr15:53089400-53089600	Flanking Active TSS	Pancreas	Pancrea
15	chr15:53089400-53089600	Flanking Bivalent TSS/Enh	Dnd41	blood
16	chr15:53089400-53090200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr15:53089400-53091200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
18	chr15:53089400-53091400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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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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