Variant report

Variant	rs62183652
Chromosome Location	chr2:190513603-190513604
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190512609..190514902-chr2:190525994..190527624,2	K562	blood:
2	chr2:190505910..190508491-chr2:190509501..190513680,4	MCF-7	breast:
3	chr2:190507159..190510939-chr2:190512994..190516291,4	K562	blood:

Variant related genes	Relation type
ENSG00000138381	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs16831821	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831873	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16831944	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16831972	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17271246	0.82[EUR][1000 genomes]
rs2164830	0.86[EUR][1000 genomes]
rs2278591	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2289405	0.83[EUR][1000 genomes]
rs56137655	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56324258	0.81[EUR][1000 genomes]
rs5742926	0.93[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs5742985	0.83[EUR][1000 genomes]
rs5743047	0.81[EUR][1000 genomes]
rs62183651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62183653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62183656	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183657	0.81[EUR][1000 genomes]
rs62183658	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62183659	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62184265	0.82[EUR][1000 genomes]
rs62184267	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62184268	0.83[EUR][1000 genomes]
rs62185869	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62185872	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62185874	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62185897	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6726636	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72920421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv979380	chr2:190507595-190520005	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62183652	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs62183652	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs62183652	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs62183652	ORMDL1	cis	Muscle Skeletal	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190506800-190522400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:190513400-190514200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr2:190513400-190514400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:190513400-190514400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:190513400-190514400	Enhancers	NHDF-Ad	bronchial
6	chr2:190513400-190514800	Enhancers	NHLF	lung
7	chr2:190513600-190514000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr2:190513600-190514000	Enhancers	Osteobl	bone
9	chr2:190513600-190514400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links