Variant report

Variant	rs1233297
Chromosome Location	chr2:190694175-190694176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190693190..190695191-chr2:190697893..190700243,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 29 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10197331	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10207346	0.88[EUR][1000 genomes]
rs10210345	0.95[CEU][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1055091	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10931430	0.90[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes]
rs10931431	0.85[EUR][1000 genomes]
rs10931433	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1132360	0.90[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs11679767	0.85[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs11685425	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1225101	0.83[JPT][hapmap]
rs1233245	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1233262	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1233265	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1233272	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1233282	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233284	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233288	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233291	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233299	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1233302	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1234834	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12471217	0.87[EUR][1000 genomes]
rs12693551	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs12693557	0.95[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12990627	0.89[EUR][1000 genomes]
rs12992061	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13002216	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13009889	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13011710	0.89[EUR][1000 genomes]
rs13035966	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1437891	0.85[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs1898560	0.82[JPT][hapmap]
rs1899025	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2017410	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2033746	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2033870	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2164832	0.85[EUR][1000 genomes]
rs2289226	0.90[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap]
rs3791767	0.82[JPT][hapmap]
rs3791770	0.82[JPT][hapmap]
rs3791773	0.82[JPT][hapmap]
rs3816196	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4525728	0.89[EUR][1000 genomes]
rs4666783	0.81[JPT][hapmap]
rs4667297	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs4667299	0.81[EUR][1000 genomes]
rs5742933	0.81[JPT][hapmap]
rs5742938	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5743061	0.81[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5743063	0.81[CEU][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6719224	0.81[JPT][hapmap]
rs6738042	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6741074	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6942	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7568449	0.89[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap]
rs7571089	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes]
rs7591929	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7592066	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7595020	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs893784	0.90[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][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	nsv3080	chr2:190661654-190706515	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:29)

SNP	Gene	Cis/trans	Tissue	Source
rs1233297	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs1233297	ASNSD1	cis	Whole Blood	GTEx
rs1233297	ORMDL1	cis	lymphoblastoid	seeQTL
rs1233297	ORMDL1	cis	Nerve Tibial	GTEx
rs1233297	ORMDL1	cis	parietal	SCAN
rs1233297	LOC51240	cis	multi-tissue	Pritchard
rs1233297	ORMDL1	cis	Heart Left Ventricle	GTEx
rs1233297	ORMDL1	cis	lesional skin	skin_eQTL
rs1233297	ORMDL1	cis	multi-tissue	Pritchard
rs1233297	PMS1	cis	parietal	SCAN
rs1233297	MFSD6	cis	cerebellum	SCAN
rs1233297	ASNSD1	cis	Artery Aorta	GTEx
rs1233297	ASNSD1	cis	parietal	SCAN
rs1233297	ORMDL1	cis	normal skin	skin_eQTL
rs1233297	PMS1	cis	cerebellum	SCAN
rs1233297	ASNSD1	Cis_1M	lymphoblastoid	RTeQTL
rs1233297	ASNSD1	cis	Thyroid	GTEx
rs1233297	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs1233297	ORMDL1	cis	Artery Tibial	GTEx
rs1233297	ORMDL1	cis	Adipose Subcutaneous	GTEx
rs1233297	ORMDL1	cis	Muscle Skeletal	GTEx
rs1233297	ORMDL1	cis	cerebellum	SCAN
rs1233297	ASNSD1	cis	Artery Tibial	GTEx
rs1233297	HIBCH	cis	parietal	SCAN
rs1233297	ORMDL1	cis	uninvolved skin	skin_eQTL
rs1233297	ASNSD1	cis	Nerve Tibial	GTEx
rs1233297	ASNSD1	cis	cerebellum	SCAN
rs1233297	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs1233297	ASNSD1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190649800-190713400	Weak transcription	Gastric	stomach
2	chr2:190650400-190711400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:190650600-190700400	Weak transcription	Hela-S3	cervix
4	chr2:190656800-190721000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:190658200-190743800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:190659800-190743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:190661400-190717800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:190662800-190719000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr2:190663000-190701600	Weak transcription	Psoas Muscle	Psoas
10	chr2:190663000-190712800	Weak transcription	Aorta	Aorta
11	chr2:190663200-190700600	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:190663200-190712400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr2:190664800-190741800	Weak transcription	Brain Angular Gyrus	brain
14	chr2:190665000-190696600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:190669400-190743800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:190669600-190709600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:190669600-190713200	Weak transcription	Ovary	ovary
18	chr2:190669800-190709000	Weak transcription	Placenta	Placenta
19	chr2:190670800-190712800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:190671000-190719600	Weak transcription	NH-A	brain
21	chr2:190676200-190712400	Weak transcription	K562	blood
22	chr2:190677000-190709400	Weak transcription	Fetal Intestine Small	intestine
23	chr2:190681000-190743000	Weak transcription	Brain Germinal Matrix	brain
24	chr2:190683800-190709800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:190684000-190700400	Weak transcription	A549	lung
26	chr2:190684000-190712600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:190684000-190712800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:190684000-190743600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:190684400-190698800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:190684400-190700600	Weak transcription	Fetal Brain Male	brain
31	chr2:190684600-190709800	Weak transcription	HMEC	breast
32	chr2:190684600-190712600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:190684600-190712600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:190685000-190694800	Weak transcription	Fetal Thymus	thymus
35	chr2:190685000-190700800	Weak transcription	Fetal Lung	lung
36	chr2:190685000-190712600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:190685000-190736400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:190685200-190694400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:190685200-190700600	Weak transcription	HSMMtube	muscle
40	chr2:190685200-190700800	Weak transcription	Fetal Brain Female	brain
41	chr2:190685200-190706200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:190685200-190708400	Weak transcription	Fetal Intestine Large	intestine
43	chr2:190685400-190696400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:190685400-190701800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:190685400-190712800	Weak transcription	Adipose Nuclei	Adipose
46	chr2:190685400-190739400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr2:190685400-190741800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:190685600-190709600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:190685600-190712800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:190685800-190695000	Weak transcription	GM12878-XiMat	blood

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