Variant report

Variant	rs4667295
Chromosome Location	chr2:190504390-190504391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1055091	0.81[JPT][hapmap]
rs10931430	0.87[JPT][hapmap]
rs1132360	0.87[JPT][hapmap]
rs11679767	0.87[JPT][hapmap]
rs1233284	0.81[JPT][hapmap]
rs1233288	0.81[JPT][hapmap]
rs1233297	0.81[JPT][hapmap]
rs12471663	0.82[AMR][1000 genomes]
rs12693551	0.87[JPT][hapmap]
rs12693557	0.87[JPT][hapmap]
rs1437891	0.87[JPT][hapmap]
rs1899025	0.81[JPT][hapmap]
rs2033870	0.87[JPT][hapmap]
rs2289226	0.87[JPT][hapmap]
rs3816196	0.81[JPT][hapmap]
rs4667297	0.87[JPT][hapmap]
rs5742938	0.81[JPT][hapmap]
rs6434355	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6756040	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6756657	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6756913	0.82[AMR][1000 genomes]
rs6761923	0.82[AMR][1000 genomes]
rs6942	0.81[JPT][hapmap]
rs7568449	0.80[CEU][hapmap];0.87[JPT][hapmap]
rs7571089	0.87[JPT][hapmap]
rs7591929	0.81[JPT][hapmap]
rs893784	0.87[JPT][hapmap]
rs9646811	0.92[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4667295	ORMDL1	cis	uninvolved skin	skin_eQTL
rs4667295	ORMDL1	cis	multi-tissue	Pritchard
rs4667295	LOC51240	cis	multi-tissue	Pritchard
rs4667295	ORMDL1	cis	normal skin	skin_eQTL
rs4667295	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs4667295	ASNSD1	cis	cerebellum	SCAN
rs4667295	ORMDL1	cis	parietal	SCAN
rs4667295	ASNSD1	cis	Whole Blood	GTEx
rs4667295	ORMDL1	cis	lesional skin	skin_eQTL
rs4667295	MFSD6	cis	cerebellum	SCAN
rs4667295	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs4667295	ASNSD1	cis	parietal	SCAN
rs4667295	ORMDL1	cis	Lymphoblastoid	GTEx
rs4667295	ORMDL1	cis	lymphoblastoid	seeQTL
rs4667295	ORMDL1	cis	brain	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190502000-190506000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:190503000-190506200	Enhancers	Fetal Intestine Large	intestine
3	chr2:190503200-190505000	Enhancers	Fetal Intestine Small	intestine
4	chr2:190503200-190506800	Enhancers	Hela-S3	cervix
5	chr2:190503400-190504400	Enhancers	Placenta	Placenta
6	chr2:190503400-190505000	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr2:190503400-190507000	Enhancers	Stomach Mucosa	stomach
8	chr2:190503600-190505800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:190503800-190505000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:190504000-190504400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr2:190504200-190505800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:190504200-190506200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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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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