Variant report

Variant	rs1898560
Chromosome Location	chr2:190612327-190612328
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: 70 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10195109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10210345	0.80[CEU][hapmap]
rs1055091	0.80[CEU][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs10931430	0.85[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs1132360	0.84[CEU][hapmap];0.81[JPT][hapmap]
rs11679767	0.80[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs11885423	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12052909	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1225101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs1233245	0.82[CEU][hapmap]
rs1233284	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs1233288	0.80[CEU][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs1233297	0.82[JPT][hapmap]
rs1233302	0.86[JPT][hapmap]
rs12618231	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12619808	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12622902	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12693551	0.80[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs12693557	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs1317751	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1437891	0.80[CEU][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs1550388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1609883	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831873	0.93[TSI][hapmap]
rs16831925	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16831939	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16831955	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899025	0.80[CEU][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap]
rs1966729	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2017410	0.82[CEU][hapmap]
rs2033746	0.80[CEU][hapmap]
rs2033870	0.80[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs2264018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2289226	0.85[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs2289404	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]
rs3762545	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3791767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3791770	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3791773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816196	0.88[JPT][hapmap]
rs4666781	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4666783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667297	0.80[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs4667306	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55675300	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55792400	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5742933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5742938	0.80[CEU][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs5742998	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743017	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5743032	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5743047	0.93[TSI][hapmap]
rs5743052	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5743061	0.94[CEU][hapmap];0.88[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs5743063	0.94[CEU][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs5743072	0.82[TSI][hapmap]
rs62184283	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62184286	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62185871	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6434363	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6434365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6717922	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6719224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6741074	0.81[AMR][1000 genomes]
rs6942	0.80[CEU][hapmap];0.88[JPT][hapmap]
rs7557519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7568449	0.81[JPT][hapmap]
rs7571089	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs7591929	0.80[CEU][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs893784	0.85[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1898560	ORMDL1	cis	Muscle Skeletal	GTEx
rs1898560	ASNSD1	cis	cerebellum	SCAN
rs1898560	ASNSD1	cis	Whole Blood	GTEx
rs1898560	ORMDL1	cis	normal skin	skin_eQTL
rs1898560	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs1898560	ORMDL1	cis	uninvolved skin	skin_eQTL
rs1898560	LOC51240	cis	multi-tissue	Pritchard
rs1898560	PMS1	cis	parietal	SCAN
rs1898560	ASNSD1	Cis_1M	lymphoblastoid	RTeQTL
rs1898560	ORMDL1	cis	parietal	SCAN
rs1898560	ORMDL1	cis	Lymphoblastoid	GTEx
rs1898560	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs1898560	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs1898560	PMS1	cis	cerebellum	SCAN
rs1898560	ORMDL1	cis	lymphoblastoid	seeQTL
rs1898560	ASNSD1	cis	parietal	SCAN
rs1898560	ORMDL1	cis	Heart Left Ventricle	GTEx
rs1898560	ORMDL1	cis	Nerve Tibial	GTEx
rs1898560	MFSD6	cis	cerebellum	SCAN
rs1898560	ORMDL1	cis	lesional skin	skin_eQTL
rs1898560	ORMDL1	cis	cerebellum	SCAN
rs1898560	ORMDL1	cis	multi-tissue	Pritchard

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

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