Variant report

Variant	rs1440006
Chromosome Location	chr2:190612339-190612340
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190524634..190527563-chr2:190610048..190612845,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ORMDL1-3	chr2:190611390-190612603	NONHSAT076063

Variant related genes	Relation type
ENSG00000138381	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1225115	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233267	0.82[LWK][hapmap]
rs1233285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1233290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831960	0.89[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352707	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2352709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3791778	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3791779	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1440006	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs1440006	ORMDL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190540800-190618400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:190541600-190617000	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:190550800-190617000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:190550800-190626800	Weak transcription	Right Ventricle	heart
5	chr2:190551200-190617000	Weak transcription	HSMM	muscle
6	chr2:190557400-190617000	Weak transcription	Brain Angular Gyrus	brain
7	chr2:190563600-190612600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:190571600-190612400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:190575000-190615800	Weak transcription	Fetal Kidney	kidney
10	chr2:190576800-190627000	Weak transcription	Pancreas	Pancrea
11	chr2:190577000-190622600	Weak transcription	Aorta	Aorta
12	chr2:190583000-190626800	Weak transcription	Psoas Muscle	Psoas
13	chr2:190589400-190626600	Weak transcription	HUVEC	blood vessel
14	chr2:190590800-190614800	Weak transcription	Esophagus	oesophagus
15	chr2:190591000-190612800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:190594800-190627000	Weak transcription	Gastric	stomach
17	chr2:190597800-190626600	Weak transcription	Fetal Heart	heart
18	chr2:190599000-190626800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:190600800-190616600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:190601400-190626800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:190602400-190617000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:190602400-190626400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:190603800-190626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:190605000-190626800	Weak transcription	Fetal Brain Male	brain
25	chr2:190606400-190612600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:190606600-190613200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:190606800-190613200	Strong transcription	Primary B cells from cord blood	blood
28	chr2:190607000-190619200	Weak transcription	NHDF-Ad	bronchial
29	chr2:190607000-190626800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:190607000-190626800	Weak transcription	NH-A	brain
31	chr2:190607400-190626800	Weak transcription	HSMMtube	muscle
32	chr2:190607800-190621000	Strong transcription	Liver	Liver
33	chr2:190607800-190622400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:190608000-190613400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:190608000-190613600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr2:190608200-190613400	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:190608400-190613000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:190608400-190613200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:190608400-190613200	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:190608400-190613600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:190608400-190620200	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr2:190608600-190612400	Strong transcription	Placenta	Placenta
43	chr2:190608600-190614400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:190608600-190626200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:190608800-190614200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr2:190609000-190612800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:190609000-190612800	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:190609000-190613600	Strong transcription	Adipose Nuclei	Adipose
49	chr2:190609000-190614600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:190609200-190612800	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links