Variant report

Variant	rs12363839
Chromosome Location	chr11:9250359-9250360
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10454487	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840170	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs10840186	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10840188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840189	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042196	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11042197	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11042215	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042217	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11042224	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042228	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042230	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042231	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[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]
rs11042232	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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042233	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042240	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042241	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042242	1.00[ASN][1000 genomes]
rs11042246	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042253	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042257	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11042259	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11042268	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs11042272	0.82[EUR][1000 genomes]
rs11607384	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12286621	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360767	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362997	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17257379	0.84[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2133215	0.89[ASW][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[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173406	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs4627079	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4910443	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap]
rs4910446	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4910447	0.86[EUR][1000 genomes]
rs55962227	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56294473	1.00[ASN][1000 genomes]
rs60693427	1.00[ASN][1000 genomes]
rs6486138	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6486204	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486209	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66554737	1.00[ASN][1000 genomes]
rs7103472	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs7113467	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs7114013	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7115283	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7115373	0.88[EUR][1000 genomes]
rs7121753	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129049	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130400	1.00[ASN][1000 genomes]
rs72850512	0.88[EUR][1000 genomes]
rs72850528	0.82[EUR][1000 genomes]
rs72850531	0.82[EUR][1000 genomes]
rs72857989	0.91[AFR][1000 genomes]
rs72859608	0.84[EUR][1000 genomes]
rs72859676	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72859678	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72859693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72861335	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72861360	0.86[EUR][1000 genomes]
rs7394454	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7394869	1.00[ASN][1000 genomes]
rs7395631	1.00[ASN][1000 genomes]
rs7396115	1.00[CHB][hapmap]
rs7396130	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7396541	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7396840	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7929621	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7936622	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938562	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7939704	0.86[EUR][1000 genomes]
rs7940872	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945570	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7949022	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7949349	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9645644	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040049	chr11:9152536-9363488	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1053045	chr11:9208881-9363488	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv540947	chr11:9208881-9363488	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12363839	OR10A6	cis	cerebellum	SCAN
rs12363839	TMEM41B	cis	multi-tissue	Pritchard
rs12363839	OR56A1	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9202600-9251200	Weak transcription	Small Intestine	intestine
2	chr11:9226000-9252000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr11:9226000-9252800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr11:9227400-9250400	Weak transcription	Fetal Stomach	stomach
5	chr11:9227600-9250600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:9230400-9253400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:9231000-9252200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:9231400-9250600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:9236000-9252200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:9236800-9250800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:9237000-9252200	Weak transcription	NHLF	lung
12	chr11:9237000-9252400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:9237000-9254000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:9237200-9251600	Weak transcription	Primary B cells from cord blood	blood
15	chr11:9237400-9252000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:9238000-9250400	Weak transcription	HepG2	liver
17	chr11:9238600-9250600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:9240200-9252200	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr11:9241400-9254200	Weak transcription	HMEC	breast
20	chr11:9241600-9250400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:9241600-9250400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr11:9241800-9250600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr11:9241800-9252800	Weak transcription	HSMM	muscle
24	chr11:9244600-9250400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr11:9244600-9251000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr11:9244600-9252600	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:9244600-9252600	Weak transcription	Fetal Brain Female	brain
28	chr11:9244800-9250400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:9244800-9250400	Weak transcription	Psoas Muscle	Psoas
30	chr11:9245400-9252800	Weak transcription	Thymus	Thymus
31	chr11:9247000-9252400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:9247000-9252600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:9247200-9250400	Weak transcription	Right Ventricle	heart
34	chr11:9247400-9252400	Enhancers	Brain Hippocampus Middle	brain
35	chr11:9247600-9250400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr11:9247600-9252200	Weak transcription	Lung	lung
37	chr11:9247600-9252200	Weak transcription	Spleen	Spleen
38	chr11:9248000-9250800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:9248200-9250600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:9248400-9251200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr11:9248600-9251800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr11:9248600-9251800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr11:9248600-9252000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr11:9248800-9250600	Weak transcription	K562	blood
45	chr11:9249000-9250400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:9249000-9252400	Enhancers	Brain Angular Gyrus	brain
47	chr11:9249000-9252400	Weak transcription	GM12878-XiMat	blood
48	chr11:9249000-9252800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr11:9249400-9252800	Enhancers	Brain Cingulate Gyrus	brain
50	chr11:9249600-9252200	Enhancers	H1 Cell Line	embryonic stem cell

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