Variant report

Variant	rs2352709
Chromosome Location	chr2:190647919-190647920
allele	A/G
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	GABPA	chr2:190647878-190649564	A549	lung:	n/a	chr2:190649206-190649217
2	GABPA	chr2:190647896-190649533	HL-60	blood:	n/a	chr2:190649206-190649217
3	POLR2A	chr2:190647769-190650571	GM12891	blood:	n/a	n/a
4	MYBL2	chr2:190647918-190649877	HepG2	liver:	n/a	n/a
5	MAZ	chr2:190647712-190649713	IMR90	lung:	n/a	chr2:190649600-190649609
6	MXI1	chr2:190646968-190650605	SK-N-SH	brain:	n/a	n/a
7	MAZ	chr2:190647839-190650051	GM12878	blood:	n/a	chr2:190649600-190649609
8	FOXA1	chr2:190647629-190648365	HepG2	liver:	n/a	chr2:190648188-190648200
9	FOXA1	chr2:190647587-190648372	HepG2	liver:	n/a	chr2:190648188-190648200
10	POLR2A	chr2:190647838-190650429	GM12878	blood:	n/a	n/a
11	GABPA	chr2:190647885-190649492	MCF-7	breast:	n/a	chr2:190649206-190649217
12	FOXA2	chr2:190647731-190647932	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:190647689-190649912	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:190632138..190639565-chr2:190646675..190650810,8	K562	blood:
2	chr2:190640380..190645016-chr2:190647065..190650284,8	MCF-7	breast:
3	chr2:190626523..190630050-chr2:190647058..190650887,5	MCF-7	breast:
4	chr2:190524324..190528374-chr2:190645867..190651485,5	K562	blood:
5	chr2:190523468..190528374-chr2:190647262..190651485,5	K562	blood:
6	chr2:190624834..190631096-chr2:190647637..190651740,7	K562	blood:
7	chr2:190624834..190630334-chr2:190647529..190650706,8	K562	blood:
8	chr2:190631446..190641228-chr2:190647618..190650786,10	MCF-7	breast:
9	chr2:190626375..190630628-chr2:190647839..190651386,6	MCF-7	breast:
10	chr2:190636758..190640017-chr2:190647080..190650145,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231145	TF binding region
PMS1	TF binding region
ENSG00000231145	Chromatin interaction
ENSG00000128694	Chromatin interaction
ENSG00000128699	Chromatin interaction
ENSG00000138381	Chromatin interaction
ENSG00000253559	Chromatin interaction
ENSG00000273240	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1225115	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1440006	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]
rs16831960	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2254146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2352707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791778	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3791779	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2352709	ORMDL1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190627800-190648200	Weak transcription	Gastric	stomach
2	chr2:190628200-190648000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:190628200-190648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:190628200-190648200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:190628400-190648000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:190628600-190648400	Weak transcription	Small Intestine	intestine
7	chr2:190641800-190648000	Weak transcription	Colonic Mucosa	Colon
8	chr2:190644000-190648200	Weak transcription	Esophagus	oesophagus
9	chr2:190644000-190648200	Weak transcription	Spleen	Spleen
10	chr2:190644200-190648200	Weak transcription	Lung	lung
11	chr2:190645800-190648000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:190646000-190648200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:190646400-190648200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr2:190646600-190648000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr2:190646800-190648000	Enhancers	Brain Substantia Nigra	brain
16	chr2:190647000-190648000	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr2:190647000-190648200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr2:190647000-190648200	Flanking Active TSS	HUVEC	blood vessel
19	chr2:190647000-190648400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:190647000-190648800	Active TSS	Right Atrium	heart
21	chr2:190647000-190650200	Active TSS	Psoas Muscle	Psoas
22	chr2:190647200-190648000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:190647200-190648000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr2:190647200-190648000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr2:190647200-190648000	Enhancers	Stomach Mucosa	stomach
26	chr2:190647200-190648200	Flanking Active TSS	Fetal Brain Male	brain
27	chr2:190647200-190648200	Flanking Active TSS	Fetal Heart	heart
28	chr2:190647200-190648400	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr2:190647200-190648400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:190647200-190648400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr2:190647200-190648600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:190647200-190649000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:190647200-190650200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:190647400-190648000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:190647400-190648000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr2:190647400-190648000	Flanking Active TSS	Brain Anterior Caudate	brain
37	chr2:190647400-190648000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:190647400-190648000	Weak transcription	Placenta	Placenta
39	chr2:190647400-190648000	Weak transcription	Left Ventricle	heart
40	chr2:190647400-190648000	Weak transcription	Ovary	ovary
41	chr2:190647400-190648000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr2:190647400-190648000	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr2:190647400-190648000	Flanking Active TSS	NH-A	brain
44	chr2:190647400-190648200	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr2:190647400-190648200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr2:190647400-190648200	Weak transcription	Pancreas	Pancrea
47	chr2:190647400-190648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:190647400-190648600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:190647400-190649600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:190647400-190649800	Active TSS	Aorta	Aorta

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