Variant report

Variant	rs4667299
Chromosome Location	chr2:190542687-190542688
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190525678..190527961-chr2:190541592..190544569,2	K562	blood:

Variant related genes	Relation type
ENSG00000138381	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10197331	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10207346	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10207536	0.80[ASN][1000 genomes]
rs10210345	0.83[ASN][1000 genomes]
rs1055091	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10931430	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931431	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10931433	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1132360	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11679767	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685425	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1233262	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1233265	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1233272	0.83[EUR][1000 genomes]
rs1233282	0.83[EUR][1000 genomes]
rs1233284	0.83[EUR][1000 genomes]
rs1233288	0.83[EUR][1000 genomes]
rs1233291	0.83[EUR][1000 genomes]
rs1233297	0.81[EUR][1000 genomes]
rs1233299	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1233302	0.80[ASN][1000 genomes]
rs1234834	0.83[EUR][1000 genomes]
rs12471217	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12471663	0.81[ASN][1000 genomes]
rs12693551	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12693557	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12990627	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12992061	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13002216	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13009889	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13011710	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13026135	0.80[EUR][1000 genomes]
rs13035966	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1437891	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1899025	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2033746	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2033870	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2289226	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816196	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4667296	0.88[ASN][1000 genomes]
rs4667297	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5742938	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6434361	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6738042	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6741074	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6756571	0.81[ASN][1000 genomes]
rs6756913	0.81[ASN][1000 genomes]
rs6761923	0.80[ASN][1000 genomes]
rs6942	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7568449	0.89[ASN][1000 genomes]
rs7571089	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7591929	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7592066	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7595020	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs893784	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs920427	0.90[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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4667299	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs4667299	ORMDL1	cis	Artery Tibial	GTEx
rs4667299	ORMDL1	cis	Muscle Skeletal	GTEx
rs4667299	ASNSD1	cis	Thyroid	GTEx
rs4667299	ORMDL1	cis	Heart Left Ventricle	GTEx
rs4667299	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs4667299	ASNSD1	cis	Artery Aorta	GTEx
rs4667299	ASNSD1	cis	Nerve Tibial	GTEx
rs4667299	ORMDL1	cis	Nerve Tibial	GTEx
rs4667299	ASNSD1	Cis_1M	lymphoblastoid	RTeQTL
rs4667299	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs4667299	ASNSD1	cis	Esophagus Muscularis	GTEx
rs4667299	ASNSD1	cis	Whole Blood	GTEx
rs4667299	ORMDL1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190530000-190542800	Strong transcription	Dnd41	blood
2	chr2:190534000-190550200	Weak transcription	K562	blood
3	chr2:190539600-190543400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:190539800-190550200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:190539800-190550200	Weak transcription	Esophagus	oesophagus
6	chr2:190539800-190550200	Weak transcription	Small Intestine	intestine
7	chr2:190540000-190546000	Weak transcription	Gastric	stomach
8	chr2:190540000-190546000	Weak transcription	Left Ventricle	heart
9	chr2:190540000-190546000	Weak transcription	Ovary	ovary
10	chr2:190540000-190550200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:190540000-190550200	Weak transcription	Fetal Thymus	thymus
12	chr2:190540000-190550400	Weak transcription	Fetal Kidney	kidney
13	chr2:190540000-190563400	Weak transcription	Aorta	Aorta
14	chr2:190540200-190543000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:190540200-190543000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:190540200-190546600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:190540200-190547800	Weak transcription	HMEC	breast
18	chr2:190540200-190550200	Weak transcription	Right Atrium	heart
19	chr2:190540200-190550200	Weak transcription	Right Ventricle	heart
20	chr2:190540200-190578000	Weak transcription	Fetal Brain Male	brain
21	chr2:190540400-190542800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:190540400-190543200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:190540400-190544600	Weak transcription	NH-A	brain
24	chr2:190540400-190546000	Weak transcription	Spleen	Spleen
25	chr2:190540400-190550200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:190540400-190550200	Weak transcription	Fetal Stomach	stomach
27	chr2:190540400-190550200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:190540400-190550200	Weak transcription	HSMMtube	muscle
29	chr2:190540400-190550200	Weak transcription	NHLF	lung
30	chr2:190540400-190550400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:190540400-190550400	Weak transcription	HSMM	muscle
32	chr2:190540400-190558400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:190540400-190564200	Weak transcription	Placenta	Placenta
34	chr2:190540400-190572000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:190540400-190576400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:190540600-190544600	Weak transcription	Fetal Heart	heart
37	chr2:190540600-190545400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:190540600-190545800	Weak transcription	Primary T cells from cord blood	blood
39	chr2:190540600-190549800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:190540600-190550200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:190540600-190550200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:190540600-190550200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:190540600-190550200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:190540600-190550200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:190540600-190550200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:190540800-190544000	Weak transcription	Primary B cells from cord blood	blood
47	chr2:190540800-190544000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:190540800-190546000	Weak transcription	Lung	lung
49	chr2:190540800-190547600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:190540800-190549600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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