Variant report

Variant	rs2289404
Chromosome Location	chr2:190636014-190636015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:190631241..190636295-chr2:190636583..190640272,4	K562	blood:
2	chr2:190626018..190630546-chr2:190631744..190636793,10	K562	blood:
3	chr2:190625930..190630327-chr2:190630673..190638393,9	K562	blood:
4	chr2:190634458..190636965-chr2:190638954..190642659,3	MCF-7	breast:
5	chr2:190634845..190637488-chr2:190645702..190648175,2	K562	blood:
6	chr2:190632138..190639565-chr2:190646675..190650810,8	K562	blood:
7	chr2:190634478..190636645-chr2:190640772..190642999,2	K562	blood:
8	chr2:190631446..190641228-chr2:190647618..190650786,10	MCF-7	breast:
9	chr2:190634789..190636320-chr2:190648047..190649597,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000064933	Chromatin interaction
ENSG00000128699	Chromatin interaction
ENSG00000128694	Chromatin interaction
ENSG00000273240	Chromatin interaction
ENSG00000253559	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10195109	0.89[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11885423	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12052909	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1225101	0.94[CEU][hapmap];0.83[JPT][hapmap]
rs1233284	0.81[JPT][hapmap]
rs12618231	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12619808	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12622902	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12693551	0.80[CHD][hapmap]
rs1317751	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1550388	1.00[ASW][hapmap];0.89[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1609883	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16831873	0.83[TSI][hapmap]
rs16831925	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16831939	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16831955	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1898560	0.89[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1966729	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2264018	0.89[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3762545	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3791767	0.93[ASW][hapmap];0.89[CEU][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3791770	0.89[CEU][hapmap];0.88[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3791773	0.89[CEU][hapmap];0.88[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816196	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs4666781	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4666783	0.92[ASW][hapmap];0.89[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667306	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55675300	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55792400	0.87[EUR][1000 genomes]
rs5742933	0.89[CEU][hapmap];0.87[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5742998	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5743017	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743032	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743047	0.83[TSI][hapmap]
rs5743052	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5743061	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs5743063	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62184283	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62184286	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62185871	0.87[EUR][1000 genomes]
rs6434363	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6434365	0.89[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6717922	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6719224	0.89[CEU][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7557519	1.00[ASW][hapmap];0.89[CEU][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2289404	ORMDL1	cis	Nerve Tibial	GTEx
rs2289404	ORMDL1	cis	parietal	SCAN
rs2289404	ORMDL1	cis	Muscle Skeletal	GTEx
rs2289404	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs2289404	ASNSD1	cis	Whole Blood	GTEx
rs2289404	MFSD6	cis	cerebellum	SCAN
rs2289404	ORMDL1	cis	cerebellum	SCAN
rs2289404	PMS1	cis	cerebellum	SCAN
rs2289404	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs2289404	ORMDL1	cis	lymphoblastoid	seeQTL
rs2289404	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs2289404	ASNSD1	cis	cerebellum	SCAN
rs2289404	PMS1	cis	parietal	SCAN
rs2289404	ORMDL1	cis	Heart Left Ventricle	GTEx
rs2289404	ASNSD1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190627800-190642800	Weak transcription	Spleen	Spleen
2	chr2:190627800-190648200	Weak transcription	Gastric	stomach
3	chr2:190628200-190638000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:190628200-190638000	Weak transcription	Right Ventricle	heart
5	chr2:190628200-190638400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:190628200-190638600	Weak transcription	Colonic Mucosa	Colon
7	chr2:190628200-190642800	Weak transcription	Lung	lung
8	chr2:190628200-190643200	Weak transcription	Esophagus	oesophagus
9	chr2:190628200-190645600	Weak transcription	Pancreas	Pancrea
10	chr2:190628200-190648000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:190628200-190648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:190628200-190648200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:190628400-190642800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:190628400-190648000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:190628600-190636200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:190628600-190637200	Weak transcription	Fetal Kidney	kidney
17	chr2:190628600-190637600	Weak transcription	Fetal Brain Female	brain
18	chr2:190628600-190638800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:190628600-190638800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:190628600-190642800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:190628600-190642800	Weak transcription	Fetal Intestine Small	intestine
22	chr2:190628600-190642800	Weak transcription	Thymus	Thymus
23	chr2:190628600-190647000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:190628600-190647200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:190628600-190647200	Weak transcription	Stomach Mucosa	stomach
26	chr2:190628600-190648400	Weak transcription	Small Intestine	intestine
27	chr2:190628800-190636200	Weak transcription	Psoas Muscle	Psoas
28	chr2:190628800-190638000	Weak transcription	Brain Angular Gyrus	brain
29	chr2:190628800-190638600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:190628800-190638800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:190628800-190639200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:190628800-190642800	Weak transcription	Fetal Stomach	stomach
33	chr2:190629000-190638000	Weak transcription	Brain Substantia Nigra	brain
34	chr2:190629000-190638600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:190629000-190644200	Weak transcription	Fetal Brain Male	brain
36	chr2:190629000-190647200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:190629200-190636200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:190629200-190638000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:190629200-190639400	Weak transcription	Hela-S3	cervix
40	chr2:190629400-190637800	Weak transcription	NHLF	lung
41	chr2:190629800-190647000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:190630000-190646600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:190630800-190647000	Strong transcription	HSMM	muscle
44	chr2:190631000-190637000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr2:190631000-190646200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:190631200-190645400	Strong transcription	Liver	Liver
47	chr2:190631200-190646200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:190631200-190647200	Strong transcription	Fetal Thymus	thymus
49	chr2:190631400-190642200	Strong transcription	NHDF-Ad	bronchial
50	chr2:190631400-190644000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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