Variant report

Variant	rs1233245
Chromosome Location	chr2:190700494-190700495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190696610..190698591-chr2:190698708..190701659,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10195109	0.84[CEU][hapmap]
rs10197331	0.83[EUR][1000 genomes]
rs10210345	0.85[CEU][hapmap]
rs1055091	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs10931430	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs10931433	0.82[EUR][1000 genomes]
rs1132360	0.90[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap]
rs11679767	0.84[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs11685425	0.82[EUR][1000 genomes]
rs1225101	0.82[CEU][hapmap]
rs1233262	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1233265	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1233272	0.84[EUR][1000 genomes]
rs1233282	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1233284	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1233288	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1233291	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1233297	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1233299	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1233302	0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1234834	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12693551	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs12693557	0.85[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap]
rs12992061	0.80[EUR][1000 genomes]
rs13002216	0.82[EUR][1000 genomes]
rs13009889	0.83[EUR][1000 genomes]
rs1437891	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1550388	0.82[CEU][hapmap]
rs1898560	0.82[CEU][hapmap]
rs1899025	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2017410	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033746	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs2033870	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2264018	0.83[CEU][hapmap]
rs2289226	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs3791767	0.82[CEU][hapmap]
rs3791770	0.84[CEU][hapmap]
rs3791773	0.84[CEU][hapmap]
rs3816196	0.89[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs4666783	0.84[CEU][hapmap]
rs4667297	0.84[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs5742933	0.89[CEU][hapmap]
rs5742938	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5743061	0.88[CEU][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5743063	0.88[CEU][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs6434365	0.84[CEU][hapmap]
rs6719224	0.82[CEU][hapmap]
rs6738042	0.83[EUR][1000 genomes]
rs6741074	0.80[EUR][1000 genomes]
rs6942	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs7557519	0.82[CEU][hapmap]
rs7568449	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7571089	0.85[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7591929	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7592066	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7595020	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs893784	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv584063	chr2:190696924-190708287	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1233245	ASNSD1	cis	Thyroid	GTEx
rs1233245	ORMDL1	cis	lesional skin	skin_eQTL
rs1233245	ORMDL1	cis	Adipose Subcutaneous	GTEx
rs1233245	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs1233245	LOC51240	cis	multi-tissue	Pritchard
rs1233245	ASNSD1	cis	Whole Blood	GTEx
rs1233245	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs1233245	ORMDL1	cis	Lymphoblastoid	GTEx
rs1233245	ASNSD1	Cis_1M	lymphoblastoid	RTeQTL
rs1233245	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs1233245	ORMDL1	cis	uninvolved skin	skin_eQTL
rs1233245	ASNSD1	cis	Esophagus Muscularis	GTEx
rs1233245	ORMDL1	cis	normal skin	skin_eQTL
rs1233245	ORMDL1	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

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	chr2:190656800-190721000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:190658200-190743800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:190659800-190743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:190661400-190717800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:190662800-190719000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:190663000-190701600	Weak transcription	Psoas Muscle	Psoas
9	chr2:190663000-190712800	Weak transcription	Aorta	Aorta
10	chr2:190663200-190700600	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:190663200-190712400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:190664800-190741800	Weak transcription	Brain Angular Gyrus	brain
13	chr2:190669400-190743800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:190669600-190709600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:190669600-190713200	Weak transcription	Ovary	ovary
16	chr2:190669800-190709000	Weak transcription	Placenta	Placenta
17	chr2:190670800-190712800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:190671000-190719600	Weak transcription	NH-A	brain
19	chr2:190676200-190712400	Weak transcription	K562	blood
20	chr2:190677000-190709400	Weak transcription	Fetal Intestine Small	intestine
21	chr2:190681000-190743000	Weak transcription	Brain Germinal Matrix	brain
22	chr2:190683800-190709800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr2:190684000-190712600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:190684000-190712800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:190684000-190743600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:190684400-190700600	Weak transcription	Fetal Brain Male	brain
27	chr2:190684600-190709800	Weak transcription	HMEC	breast
28	chr2:190684600-190712600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:190684600-190712600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:190685000-190700800	Weak transcription	Fetal Lung	lung
31	chr2:190685000-190712600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:190685000-190736400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:190685200-190700600	Weak transcription	HSMMtube	muscle
34	chr2:190685200-190700800	Weak transcription	Fetal Brain Female	brain
35	chr2:190685200-190706200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:190685200-190708400	Weak transcription	Fetal Intestine Large	intestine
37	chr2:190685400-190701800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr2:190685400-190712800	Weak transcription	Adipose Nuclei	Adipose
39	chr2:190685400-190739400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:190685400-190741800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr2:190685600-190709600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:190685600-190712800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:190685800-190702000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr2:190685800-190708600	Weak transcription	Liver	Liver
45	chr2:190685800-190708800	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:190685800-190709600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr2:190686000-190711400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr2:190687000-190706800	Weak transcription	Left Ventricle	heart
49	chr2:190687000-190712800	Weak transcription	Thymus	Thymus
50	chr2:190687000-190724400	Weak transcription	Esophagus	oesophagus

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