Variant report

Variant	rs3828267
Chromosome Location	chr2:190531615-190531616
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190529439..190532405-chr2:190545827..190547782,2	MCF-7	breast:
2	chr2:190525922..190529074-chr2:190530082..190533259,4	K562	blood:

Variant related genes	Relation type
ENSG00000138381	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12053254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12614807	0.90[ASN][1000 genomes]
rs12618246	1.00[JPT][hapmap]
rs12618262	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs12620204	0.90[ASN][1000 genomes]
rs3762543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4643578	0.92[ASN][1000 genomes]
rs4666782	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap]
rs4667304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4920657	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs5742967	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap]
rs5742981	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs5743004	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs5743030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs5743044	0.86[EUR][1000 genomes]
rs5743100	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs5743112	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs5743116	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs5743117	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs6434358	0.90[ASN][1000 genomes]
rs6434360	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6707560	0.91[CHD][hapmap]
rs6718862	0.90[ASN][1000 genomes]
rs733318	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap]
rs73979023	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979024	1.00[EUR][1000 genomes];1.00[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3828267	ORMDL1	cis	multi-tissue	Pritchard
rs3828267	ORMDL1	cis	Lymphoblastoid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190527000-190534800	Weak transcription	Lung	lung
2	chr2:190527400-190532000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:190527400-190532200	Weak transcription	Left Ventricle	heart
4	chr2:190527400-190533000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:190527400-190533600	Weak transcription	K562	blood
6	chr2:190527400-190537400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:190527400-190538400	Weak transcription	Pancreas	Pancrea
8	chr2:190527400-190538400	Weak transcription	Right Ventricle	heart
9	chr2:190527400-190538600	Weak transcription	Esophagus	oesophagus
10	chr2:190527400-190538600	Weak transcription	Gastric	stomach
11	chr2:190527400-190539000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:190527600-190532000	Weak transcription	Aorta	Aorta
13	chr2:190527600-190532600	Weak transcription	Colonic Mucosa	Colon
14	chr2:190527600-190532600	Weak transcription	Fetal Intestine Small	intestine
15	chr2:190527600-190532800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:190527600-190538600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:190527600-190538600	Weak transcription	Spleen	Spleen
18	chr2:190527600-190539200	Weak transcription	Small Intestine	intestine
19	chr2:190527800-190531800	Weak transcription	Thymus	Thymus
20	chr2:190527800-190532200	Weak transcription	NHEK	skin
21	chr2:190527800-190532800	Weak transcription	Brain Substantia Nigra	brain
22	chr2:190527800-190533000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:190527800-190538400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:190527800-190538400	Weak transcription	Psoas Muscle	Psoas
25	chr2:190527800-190538600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:190528200-190537600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:190528200-190541600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:190528400-190532600	Weak transcription	Fetal Brain Male	brain
29	chr2:190528400-190536000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:190528400-190537400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:190528600-190531800	Weak transcription	Hela-S3	cervix
32	chr2:190528600-190532200	Weak transcription	Fetal Stomach	stomach
33	chr2:190528600-190538000	Weak transcription	Fetal Heart	heart
34	chr2:190528600-190539600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:190528800-190537000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:190529000-190536000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:190529000-190537000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:190529000-190537200	Strong transcription	Placenta	Placenta
39	chr2:190529000-190537800	Strong transcription	HSMM	muscle
40	chr2:190529200-190537200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr2:190529400-190535000	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:190529400-190537200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr2:190529600-190531800	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:190529600-190537000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:190529600-190537200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:190529800-190532400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:190529800-190533600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:190529800-190534400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr2:190529800-190534600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:190529800-190537200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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