Variant report

Variant	rs912466
Chromosome Location	chr10:96271840-96271841
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1018602	0.84[ASN][1000 genomes]
rs10786168	0.91[MEX][hapmap];0.86[TSI][hapmap]
rs10786169	0.80[JPT][hapmap]
rs1079504	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10882460	0.91[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs10882463	0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs10882469	0.84[EUR][1000 genomes]
rs10882470	0.81[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10882471	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10882473	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10882474	0.91[MEX][hapmap];0.86[TSI][hapmap]
rs10882481	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11187937	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11187939	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11187944	0.82[EUR][1000 genomes]
rs11187948	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11187952	0.84[LWK][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs11187958	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11187966	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11187972	0.83[EUR][1000 genomes]
rs11187973	0.86[EUR][1000 genomes]
rs11187980	0.83[ASW][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11187996	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11187998	0.85[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11188005	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11188009	0.83[ASW][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs11188012	0.80[JPT][hapmap]
rs11188015	0.83[EUR][1000 genomes]
rs11188016	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11188017	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11188019	0.80[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap]
rs11188026	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11188030	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11188038	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188039	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188040	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188041	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11527881	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11592354	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11638	0.80[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs12218213	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12218216	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12219906	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12220588	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12221475	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12570013	0.84[ASN][1000 genomes]
rs12572040	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12573638	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12762574	0.85[EUR][1000 genomes]
rs1359263	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[ASN][1000 genomes]
rs1749352	0.81[EUR][1000 genomes]
rs1749355	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1749356	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1854034	0.81[EUR][1000 genomes]
rs1886272	0.80[EUR][1000 genomes]
rs1889485	0.85[EUR][1000 genomes]
rs1889486	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1931757	0.80[JPT][hapmap]
rs1969815	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1977290	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1977291	0.80[JPT][hapmap]
rs1980741	0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs2012670	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2095380	0.84[EUR][1000 genomes]
rs2148553	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2244241	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2265362	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2265364	0.82[EUR][1000 genomes]
rs2274417	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2281791	0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs2860760	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2860821	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2901764	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2901765	0.82[EUR][1000 genomes]
rs34814196	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35774063	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3740358	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4316436	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4351744	0.80[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs4421688	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4611135	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs479664	0.87[EUR][1000 genomes]
rs4918333	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4918401	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4918402	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4918403	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4918409	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4918411	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4918417	0.84[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4918418	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4918419	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs493088	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs517784	0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs522111	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs541704	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs542540	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs556055	0.82[EUR][1000 genomes]
rs56020662	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs576517	0.90[EUR][1000 genomes]
rs581165	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6583943	0.85[EUR][1000 genomes]
rs6583944	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6583945	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68046102	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs692872	0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs701885	0.91[MEX][hapmap];0.82[TSI][hapmap]
rs7068337	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7073639	0.82[EUR][1000 genomes]
rs7078236	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7078478	0.80[JPT][hapmap]
rs7078811	0.80[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs7083898	0.80[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7086462	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7087472	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7089094	0.81[EUR][1000 genomes]
rs7393251	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7898330	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7906843	0.89[LWK][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.83[YRI][hapmap]
rs7906968	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7913343	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs7921721	0.83[ASW][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8181426	0.83[AFR][1000 genomes]
rs9420641	0.81[EUR][1000 genomes]
rs945123	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs955694	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9633699	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription 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	14 gene(s)	inside rSNPs	diseases
2	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1053747	chr10:96211618-96366396	Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs912466	HELLS	cis	cerebellum	SCAN
rs912466	C19orf22	trans	cerebellum	SCAN
rs912466	KIF11	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96211600-96292200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:96219800-96283400	Weak transcription	Lung	lung
3	chr10:96223200-96293600	Weak transcription	NHDF-Ad	bronchial
4	chr10:96238200-96273400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr10:96244000-96282600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:96244400-96283600	Weak transcription	Pancreas	Pancrea
7	chr10:96244400-96304600	Weak transcription	Aorta	Aorta
8	chr10:96248000-96273800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr10:96249200-96286200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:96249400-96288600	Weak transcription	Gastric	stomach
11	chr10:96250400-96281000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr10:96250800-96281000	Weak transcription	Brain Angular Gyrus	brain
13	chr10:96250800-96294000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr10:96250800-96297400	Weak transcription	Small Intestine	intestine
15	chr10:96256200-96283600	Weak transcription	Osteobl	bone
16	chr10:96256800-96283800	Weak transcription	Liver	Liver
17	chr10:96257000-96293400	Weak transcription	HepG2	liver
18	chr10:96261000-96304400	Weak transcription	NH-A	brain
19	chr10:96264200-96296800	Weak transcription	Brain Germinal Matrix	brain
20	chr10:96266000-96304600	Weak transcription	Fetal Kidney	kidney
21	chr10:96266800-96274400	Strong transcription	HSMM	muscle
22	chr10:96267400-96303800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr10:96267800-96280800	Weak transcription	Brain Anterior Caudate	brain
24	chr10:96268200-96283400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:96268400-96304400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr10:96268600-96274000	Strong transcription	Fetal Intestine Large	intestine
27	chr10:96268600-96279200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:96268800-96274000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr10:96268800-96285800	Weak transcription	Fetal Lung	lung
30	chr10:96268800-96297200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:96268800-96304400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr10:96269200-96283600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr10:96269400-96273000	Weak transcription	Fetal Intestine Small	intestine
34	chr10:96269400-96283800	Weak transcription	Ovary	ovary
35	chr10:96269400-96285800	Weak transcription	Colon Smooth Muscle	Colon
36	chr10:96269600-96292000	Weak transcription	Brain Hippocampus Middle	brain
37	chr10:96269800-96274000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr10:96270200-96285000	Weak transcription	Right Ventricle	heart
39	chr10:96270200-96304200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr10:96270400-96278800	Strong transcription	Fetal Stomach	stomach
41	chr10:96270400-96281000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr10:96270600-96272600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr10:96270600-96278600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:96270800-96285600	Weak transcription	Esophagus	oesophagus
45	chr10:96271000-96272000	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr10:96271000-96272000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr10:96271000-96272400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:96271000-96272400	Strong transcription	Adipose Nuclei	Adipose
49	chr10:96271000-96272600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr10:96271400-96272000	Strong transcription	Placenta	Placenta

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