Variant report

Variant	rs12417962
Chromosome Location	chr11:45241958-45241959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10160228	0.87[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11038347	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11038348	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12271122	0.87[AMR][1000 genomes]
rs12289677	0.81[AMR][1000 genomes]
rs12573851	0.90[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12573853	0.93[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2012408	0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2863164	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2863165	0.88[CHB][hapmap]
rs34007448	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3740784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758724	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4755949	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4755959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs61880311	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61880320	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61880323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7105035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7108362	0.82[CHD][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.88[AMR][1000 genomes]
rs7125368	0.86[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12417962	OR4X2	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45205800-45251800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr11:45206000-45247800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr11:45206600-45251600	Weak transcription	HepG2	liver
4	chr11:45210200-45247600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:45210200-45251600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:45224800-45247800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:45227400-45242600	Weak transcription	Liver	Liver
8	chr11:45227800-45247400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:45229000-45246600	Weak transcription	Primary T cells from cord blood	blood
10	chr11:45231400-45242400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr11:45232000-45247600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:45232200-45247600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:45232200-45247800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:45232400-45247000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:45232400-45247600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:45232400-45247800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr11:45232400-45247800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr11:45232400-45247800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:45232400-45250400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:45232600-45245200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:45232600-45247000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:45232600-45255200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:45232800-45246000	Weak transcription	Colon Smooth Muscle	Colon
24	chr11:45232800-45247200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:45232800-45248000	Weak transcription	Fetal Brain Male	brain
26	chr11:45233000-45245000	Weak transcription	Hela-S3	cervix
27	chr11:45233000-45245400	Weak transcription	Brain Substantia Nigra	brain
28	chr11:45233600-45248800	Weak transcription	Fetal Heart	heart
29	chr11:45233800-45246400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr11:45234600-45242400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:45234800-45247000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:45235000-45245000	Weak transcription	Brain Angular Gyrus	brain
33	chr11:45235000-45247200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr11:45235000-45247200	Weak transcription	Placenta	Placenta
35	chr11:45235200-45242200	Weak transcription	Fetal Brain Female	brain
36	chr11:45235200-45242600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr11:45235200-45245600	Weak transcription	Gastric	stomach
38	chr11:45235200-45246000	Weak transcription	A549	lung
39	chr11:45235200-45246400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:45235200-45247600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:45235200-45247600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:45235200-45247600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:45235200-45247800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:45235400-45246000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:45235400-45246000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:45235400-45247600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:45235600-45245200	Weak transcription	Esophagus	oesophagus
48	chr11:45235600-45245400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:45235600-45245600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr11:45235600-45247800	Weak transcription	Colonic Mucosa	Colon

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