Variant report

Variant	rs5743002
Chromosome Location	chr2:190664824-190664825
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190655142..190657284-chr2:190662768..190665130,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064933	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1233264	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12622938	0.85[EUR][1000 genomes]
rs16831841	0.85[EUR][1000 genomes]
rs16831880	1.00[AMR][1000 genomes]
rs16831887	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16831909	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831964	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17199060	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3791772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4666785	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667307	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5742959	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5742960	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5743006	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv3080	chr2:190661654-190706515	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5743002	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190649800-190667200	Weak transcription	Pancreas	Pancrea
2	chr2:190649800-190675200	Weak transcription	Esophagus	oesophagus
3	chr2:190649800-190713400	Weak transcription	Gastric	stomach
4	chr2:190650000-190688200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:190650200-190668200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:190650200-190669200	Weak transcription	Right Ventricle	heart
7	chr2:190650200-190673000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:190650200-190673200	Weak transcription	Small Intestine	intestine
9	chr2:190650400-190666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:190650400-190667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:190650400-190670400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:190650400-190675800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:190650400-190686800	Weak transcription	Thymus	Thymus
14	chr2:190650400-190688400	Weak transcription	Colonic Mucosa	Colon
15	chr2:190650400-190689800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:190650400-190711400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:190650600-190668200	Weak transcription	Fetal Brain Female	brain
18	chr2:190650600-190683200	Weak transcription	Fetal Brain Male	brain
19	chr2:190650600-190688800	Weak transcription	Fetal Heart	heart
20	chr2:190650600-190693200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:190650600-190700400	Weak transcription	Hela-S3	cervix
22	chr2:190650800-190675200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:190651000-190673000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:190651000-190673400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:190651200-190673800	Weak transcription	Brain Germinal Matrix	brain
26	chr2:190653400-190673000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:190655000-190671800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:190656200-190670800	Strong transcription	HepG2	liver
29	chr2:190656200-190673000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:190656200-190677800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:190656400-190665000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:190656800-190666600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:190656800-190685000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:190656800-190721000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:190657600-190665000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:190657600-190669400	Strong transcription	Fetal Thymus	thymus
37	chr2:190657800-190665000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:190657800-190665000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:190658000-190671400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:190658200-190743800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:190659000-190685000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:190659200-190668800	Weak transcription	Ovary	ovary
43	chr2:190659200-190681200	Weak transcription	Spleen	Spleen
44	chr2:190659800-190686800	Weak transcription	Fetal Stomach	stomach
45	chr2:190659800-190743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:190661000-190665000	Strong transcription	Fetal Lung	lung
47	chr2:190661000-190674400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr2:190661200-190673000	Weak transcription	Fetal Intestine Small	intestine
49	chr2:190661400-190670400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:190661400-190717800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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