Variant report

Variant	rs10896788
Chromosome Location	chr11:58292976-58292977
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	chr11:58292350..58294011-chr11:58343691..58345375,2	K562	blood:
2	chr11:58287109..58289381-chr11:58290390..58293298,3	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10792172	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs10896774	0.85[AMR][1000 genomes]
rs10896775	0.83[AMR][1000 genomes]
rs10896785	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10896787	0.91[AFR][1000 genomes];0.96[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];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896795	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10896796	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229409	0.84[CHB][hapmap];0.92[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	0.82[AMR][1000 genomes]
rs11229463	0.83[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs11229505	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229512	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229519	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229543	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11229545	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229555	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11530830	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11601687	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11603890	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11605269	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605297	0.82[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];0.97[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12269745	0.85[AMR][1000 genomes]
rs12274866	0.85[AMR][1000 genomes]
rs12279895	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12280114	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12283414	0.85[AMR][1000 genomes]
rs12285111	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes]
rs12286421	0.85[AMR][1000 genomes]
rs12289198	0.85[AMR][1000 genomes]
rs12290089	0.85[AMR][1000 genomes]
rs12291551	0.85[AMR][1000 genomes]
rs12294062	0.85[AMR][1000 genomes]
rs12786744	0.87[AMR][1000 genomes]
rs12787765	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12797488	0.87[AMR][1000 genomes]
rs12799215	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12800710	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12802819	0.85[AMR][1000 genomes]
rs12802960	0.85[AMR][1000 genomes]
rs12803648	0.82[AMR][1000 genomes]
rs12808544	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17474373	0.87[AMR][1000 genomes]
rs17567523	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1893902	0.83[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap]
rs1938598	0.88[AMR][1000 genomes];0.86[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];0.85[YRI][hapmap];0.87[AMR][1000 genomes]
rs2275993	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276153	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2298608	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3168135	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35279927	0.85[AMR][1000 genomes]
rs4127353	0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs4323891	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4347409	0.85[AMR][1000 genomes]
rs4506677	0.85[AMR][1000 genomes]
rs4517537	0.85[AMR][1000 genomes]
rs4579945	0.85[AMR][1000 genomes]
rs6591475	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes]
rs7102510	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7102852	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7110210	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7925560	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7927966	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7931394	0.85[AMR][1000 genomes]
rs8373	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.86[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
rs10896788	OR4C6	cis	cerebellum	SCAN
rs10896788	MS4A10	cis	cerebellum	SCAN
rs10896788	SERPING1	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58290400-58294400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:58290400-58295400	Weak transcription	Right Ventricle	heart
3	chr11:58291200-58293400	Enhancers	Fetal Thymus	thymus
4	chr11:58291400-58293000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:58291400-58293400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:58291400-58293400	Flanking Active TSS	Dnd41	blood
7	chr11:58291600-58293200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr11:58291600-58293800	Enhancers	Thymus	Thymus
9	chr11:58291600-58293800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr11:58291600-58294000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:58291800-58293000	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr11:58291800-58293000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr11:58291800-58293000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:58291800-58293200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr11:58291800-58294400	Weak transcription	Psoas Muscle	Psoas
16	chr11:58291800-58297200	Weak transcription	Pancreas	Pancrea
17	chr11:58292000-58293000	Enhancers	Duodenum Mucosa	Duodenum
18	chr11:58292000-58293400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr11:58292000-58294800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:58292000-58295000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:58292000-58295000	Weak transcription	Lung	lung
22	chr11:58292000-58295000	Weak transcription	Spleen	Spleen
23	chr11:58292000-58295200	Weak transcription	Small Intestine	intestine
24	chr11:58292000-58295400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:58292000-58297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:58292000-58299200	Weak transcription	Esophagus	oesophagus
27	chr11:58292000-58299400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr11:58292000-58314000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:58292000-58317200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr11:58292000-58317600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:58292200-58294200	Weak transcription	Adipose Nuclei	Adipose
32	chr11:58292200-58294400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:58292200-58294400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr11:58292200-58294400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:58292200-58294400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr11:58292200-58294400	Weak transcription	Brain Substantia Nigra	brain
37	chr11:58292200-58294400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:58292200-58294400	Weak transcription	Fetal Muscle Leg	muscle
39	chr11:58292200-58294400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:58292200-58294400	Weak transcription	HMEC	breast
41	chr11:58292200-58294400	Weak transcription	HSMM	muscle
42	chr11:58292200-58294600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr11:58292200-58294800	Weak transcription	Brain Anterior Caudate	brain
44	chr11:58292200-58294800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:58292200-58294800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:58292200-58295000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:58292200-58295000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:58292200-58295000	Weak transcription	Aorta	Aorta
49	chr11:58292200-58295000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr11:58292200-58295000	Weak transcription	Fetal Intestine Large	intestine

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