Variant report

Variant	rs12618262
Chromosome Location	chr2:190708073-190708074
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	chr2:190707467..190709544-chr2:190709954..190711600,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1030136	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12053254	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs16832155	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16832158	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256552	0.85[JPT][hapmap]
rs256563	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs256564	0.86[JPT][hapmap]
rs256567	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs256572	0.82[ASN][1000 genomes]
rs256580	0.82[ASN][1000 genomes]
rs3762543	0.85[CEU][hapmap]
rs3828267	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs4666782	0.85[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs4667304	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs4853634	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4920654	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4920657	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4920658	0.85[EUR][1000 genomes]
rs4920660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4920662	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5742967	0.90[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs5742981	0.85[CEU][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs5743004	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs5743030	0.85[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs5743044	0.97[EUR][1000 genomes]
rs5743100	0.85[CEU][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes]
rs5743112	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5743116	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743117	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5743202	0.87[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5743208	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6736360	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs733318	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73979023	0.83[EUR][1000 genomes]
rs73979024	0.83[EUR][1000 genomes]

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	nsv584063	chr2:190696924-190708287	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv875617	chr2:190701869-190724141	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12618262	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs12618262	TNFSF10	trans	lymphoblastoid	RTeQTL
rs12618262	ORMDL1	cis	multi-tissue	Pritchard
rs12618262	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 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	chr2:190656800-190721000	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	chr2:190663000-190712800	Weak transcription	Aorta	Aorta
9	chr2:190663200-190712400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:190664800-190741800	Weak transcription	Brain Angular Gyrus	brain
11	chr2:190669400-190743800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:190669600-190709600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:190669600-190713200	Weak transcription	Ovary	ovary
14	chr2:190669800-190709000	Weak transcription	Placenta	Placenta
15	chr2:190670800-190712800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:190671000-190719600	Weak transcription	NH-A	brain
17	chr2:190676200-190712400	Weak transcription	K562	blood
18	chr2:190677000-190709400	Weak transcription	Fetal Intestine Small	intestine
19	chr2:190681000-190743000	Weak transcription	Brain Germinal Matrix	brain
20	chr2:190683800-190709800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:190684000-190712600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:190684000-190712800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:190684000-190743600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:190684600-190709800	Weak transcription	HMEC	breast
25	chr2:190684600-190712600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:190684600-190712600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:190685000-190712600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:190685000-190736400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:190685200-190708400	Weak transcription	Fetal Intestine Large	intestine
30	chr2:190685400-190712800	Weak transcription	Adipose Nuclei	Adipose
31	chr2:190685400-190739400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:190685400-190741800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:190685600-190709600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:190685600-190712800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:190685800-190708600	Weak transcription	Liver	Liver
36	chr2:190685800-190708800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr2:190685800-190709600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:190686000-190711400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr2:190687000-190712800	Weak transcription	Thymus	Thymus
40	chr2:190687000-190724400	Weak transcription	Esophagus	oesophagus
41	chr2:190687000-190738400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:190687000-190738400	Weak transcription	Lung	lung
43	chr2:190687200-190710200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:190687200-190710400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:190687400-190708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:190691000-190709600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:190691000-190709800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:190691000-190712800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:190691000-190744200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:190691200-190708200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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