Variant report

Variant	rs4667307
Chromosome Location	chr2:190652094-190652095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:190652022-190652295	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:190647276..190650554-chr2:190651285..190655596,9	MCF-7	breast:
2	chr2:190651111..190653686-chr2:190669212..190673503,3	K562	blood:
3	chr2:190649682..190653858-chr2:190657943..190661151,4	K562	blood:
4	chr2:190626395..190628968-chr2:190652066..190655379,3	K562	blood:

Variant related genes	Relation type
ORMDL1	TF binding region
PMS1	TF binding region
ENSG00000064933	Chromatin interaction
ENSG00000128699	Chromatin interaction
ENSG00000253559	Chromatin interaction
ENSG00000128694	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1233264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622938	0.82[EUR][1000 genomes]
rs16831841	0.82[EUR][1000 genomes]
rs16831887	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs16831909	1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16831964	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16832035	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17199060	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2243876	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs256561	1.00[MEX][hapmap]
rs3791769	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3791772	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4666785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5742960	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5743002	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5743006	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5743010	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5743022	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6707560	1.00[TSI][hapmap]
rs6709840	0.91[YRI][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	nsv875616	chr2:190650460-190656614	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4667307	ORMDL1	cis	lymphoblastoid	seeQTL
rs4667307	ORMDL1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190649600-190656200	Weak transcription	Spleen	Spleen
2	chr2:190649600-190658600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:190649800-190657600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:190649800-190658600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:190649800-190662200	Weak transcription	Aorta	Aorta
6	chr2:190649800-190662200	Weak transcription	Left Ventricle	heart
7	chr2:190649800-190662800	Weak transcription	Lung	lung
8	chr2:190649800-190667200	Weak transcription	Pancreas	Pancrea
9	chr2:190649800-190675200	Weak transcription	Esophagus	oesophagus
10	chr2:190649800-190713400	Weak transcription	Gastric	stomach
11	chr2:190650000-190656000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:190650000-190657000	Weak transcription	Placenta	Placenta
13	chr2:190650000-190688200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:190650200-190656400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:190650200-190656800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr2:190650200-190657600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:190650200-190658600	Weak transcription	Ovary	ovary
18	chr2:190650200-190662800	Weak transcription	Psoas Muscle	Psoas
19	chr2:190650200-190668200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:190650200-190669200	Weak transcription	Right Ventricle	heart
21	chr2:190650200-190673000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:190650200-190673200	Weak transcription	Small Intestine	intestine
23	chr2:190650400-190652200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:190650400-190652400	Weak transcription	NHDF-Ad	bronchial
25	chr2:190650400-190652600	Weak transcription	Liver	Liver
26	chr2:190650400-190652800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:190650400-190653400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:190650400-190656200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:190650400-190656400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr2:190650400-190656400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr2:190650400-190656400	Weak transcription	Brain Anterior Caudate	brain
32	chr2:190650400-190656400	Weak transcription	Fetal Intestine Large	intestine
33	chr2:190650400-190657000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:190650400-190657600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:190650400-190657600	Weak transcription	Primary T cells from cord blood	blood
36	chr2:190650400-190657600	Weak transcription	Brain Angular Gyrus	brain
37	chr2:190650400-190657600	Weak transcription	Fetal Intestine Small	intestine
38	chr2:190650400-190659600	Weak transcription	HSMMtube	muscle
39	chr2:190650400-190662200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:190650400-190662200	Weak transcription	Brain Substantia Nigra	brain
41	chr2:190650400-190662600	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:190650400-190662800	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:190650400-190664600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr2:190650400-190666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:190650400-190667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr2:190650400-190670400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:190650400-190675800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:190650400-190686800	Weak transcription	Thymus	Thymus
49	chr2:190650400-190688400	Weak transcription	Colonic Mucosa	Colon
50	chr2:190650400-190689800	Weak transcription	Rectal Smooth Muscle	rectum

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