Variant report

Variant	rs11605297
Chromosome Location	chr11:58296806-58296807
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10792172	0.85[LWK][hapmap];0.88[YRI][hapmap]
rs10896774	0.87[AMR][1000 genomes]
rs10896775	0.85[AMR][1000 genomes]
rs10896785	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10896787	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896788	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896794	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896795	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10896796	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229409	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs11229410	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229411	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229412	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229413	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229423	0.83[AMR][1000 genomes]
rs11229463	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs11229505	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229512	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229519	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229543	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11229545	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229555	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11530830	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11601687	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11603890	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11605269	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12269745	0.87[AMR][1000 genomes]
rs12274866	0.87[AMR][1000 genomes]
rs12279895	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12280114	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12283414	0.87[AMR][1000 genomes]
rs12285111	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes]
rs12286421	0.87[AMR][1000 genomes]
rs12289198	0.87[AMR][1000 genomes]
rs12290089	0.87[AMR][1000 genomes]
rs12291551	0.87[AMR][1000 genomes]
rs12294062	0.87[AMR][1000 genomes]
rs12786744	0.89[AMR][1000 genomes]
rs12787765	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12797488	0.89[AMR][1000 genomes]
rs12799215	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12800710	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12802819	0.87[AMR][1000 genomes]
rs12802960	0.87[AMR][1000 genomes]
rs12803648	0.83[AMR][1000 genomes]
rs12808544	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17474373	0.89[AMR][1000 genomes]
rs17567523	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1893902	0.83[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1938598	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1938637	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs1986404	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes]
rs2275993	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276153	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2298608	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3168135	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35279927	0.87[AMR][1000 genomes]
rs4127353	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4323891	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4347409	0.87[AMR][1000 genomes]
rs4506677	0.87[AMR][1000 genomes]
rs4517537	0.87[AMR][1000 genomes]
rs4519112	0.80[AMR][1000 genomes]
rs4579945	0.87[AMR][1000 genomes]
rs6591475	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes]
rs7102510	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7102852	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7110210	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7925560	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7927966	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7931394	0.87[AMR][1000 genomes]
rs8373	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][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	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11605297	OR4C6	cis	cerebellum	SCAN
rs11605297	MS4A10	cis	cerebellum	SCAN
rs11605297	SERPING1	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58291800-58297200	Weak transcription	Pancreas	Pancrea
2	chr11:58292000-58297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:58292000-58299200	Weak transcription	Esophagus	oesophagus
4	chr11:58292000-58299400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:58292000-58314000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr11:58292000-58317200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:58292000-58317600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:58292200-58297200	Weak transcription	Brain Hippocampus Middle	brain
9	chr11:58292200-58297400	Weak transcription	Fetal Intestine Small	intestine
10	chr11:58292200-58297800	Weak transcription	Colonic Mucosa	Colon
11	chr11:58292200-58299200	Weak transcription	NHLF	lung
12	chr11:58292200-58299800	Weak transcription	NH-A	brain
13	chr11:58292200-58307200	Weak transcription	NHDF-Ad	bronchial
14	chr11:58292200-58311400	Weak transcription	Colon Smooth Muscle	Colon
15	chr11:58292200-58312200	Weak transcription	Placenta	Placenta
16	chr11:58292200-58312400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:58292200-58314000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:58292200-58316600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:58292200-58316600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr11:58292200-58317200	Weak transcription	Brain Angular Gyrus	brain
21	chr11:58292200-58317200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:58292200-58317200	Weak transcription	Fetal Kidney	kidney
23	chr11:58292200-58317400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:58292200-58327400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:58292600-58313800	Weak transcription	Osteobl	bone
26	chr11:58292600-58315000	Weak transcription	Fetal Lung	lung
27	chr11:58293000-58297400	Weak transcription	Gastric	stomach
28	chr11:58293000-58301800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr11:58293200-58297400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:58293200-58297800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:58293400-58317000	Weak transcription	Fetal Heart	heart
32	chr11:58293400-58317200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:58293800-58297400	Strong transcription	Fetal Thymus	thymus
34	chr11:58293800-58317200	Weak transcription	Brain Germinal Matrix	brain
35	chr11:58294000-58297400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:58294000-58297400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:58294200-58297600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:58294200-58301200	Strong transcription	Adipose Nuclei	Adipose
39	chr11:58294400-58300000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:58294400-58301000	Strong transcription	Liver	Liver
41	chr11:58294600-58297200	Strong transcription	Primary B cells from peripheral blood	blood
42	chr11:58294600-58299800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr11:58294600-58314000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:58294800-58297400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:58294800-58297600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr11:58294800-58302800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr11:58295000-58297200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:58295000-58299200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr11:58295200-58297400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:58295200-58299200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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