Variant report

Variant	rs10882460
Chromosome Location	chr10:96211514-96211515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10786168	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[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];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10786169	1.00[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs1079504	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10882452	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10882454	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10882463	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];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882469	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10882470	0.91[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs10882471	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10882473	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10882474	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs10882477	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs11187937	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187938	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11187939	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187940	0.92[JPT][hapmap]
rs11187944	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11187948	0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11187952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11187958	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11187960	1.00[JPT][hapmap]
rs11187966	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11187972	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11187973	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11187980	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11187985	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11187996	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11188009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11188012	0.83[JPT][hapmap]
rs11188019	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs11188020	1.00[JPT][hapmap]
rs11188040	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs11527881	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11592354	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11638	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs12218213	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12218216	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12219906	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs12220588	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs12221475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12572040	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12573638	0.81[EUR][1000 genomes]
rs12762574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1326839	0.94[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs1334595	1.00[JPT][hapmap]
rs1359263	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1749352	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1749355	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1749356	0.82[EUR][1000 genomes]
rs1854035	0.82[EUR][1000 genomes]
rs1886272	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1889485	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1889486	0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1931757	0.83[JPT][hapmap]
rs1969815	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1977288	1.00[JPT][hapmap]
rs1977291	0.83[JPT][hapmap]
rs1980741	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2095380	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2244241	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2265362	0.83[EUR][1000 genomes]
rs2265364	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2274096	0.85[EUR][1000 genomes]
rs2274417	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs2281791	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2860760	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2860821	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs2901764	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2901765	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3740358	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs3758522	0.80[EUR][1000 genomes]
rs3758523	0.83[EUR][1000 genomes]
rs3781262	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs4316436	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4351744	0.84[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4611135	0.83[EUR][1000 genomes]
rs480032	1.00[JPT][hapmap]
rs4917505	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4918333	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4918402	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes]
rs4918404	0.85[EUR][1000 genomes]
rs4918409	0.85[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs4918419	0.85[CEU][hapmap]
rs493088	0.81[EUR][1000 genomes]
rs517784	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs522111	0.82[EUR][1000 genomes]
rs541704	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs542540	0.81[EUR][1000 genomes]
rs555782	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs556055	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56020662	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs576517	0.81[EUR][1000 genomes]
rs581165	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6583942	1.00[JPT][hapmap]
rs6583943	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6583944	0.85[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs6583946	0.83[EUR][1000 genomes]
rs692872	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs701885	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs7073639	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7075182	0.88[JPT][hapmap]
rs7078236	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7078478	0.83[JPT][hapmap]
rs7078811	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs7079934	0.85[EUR][1000 genomes]
rs7083898	1.00[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7086462	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7087472	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7087798	0.83[JPT][hapmap]
rs7089094	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7092129	1.00[JPT][hapmap]
rs7393251	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7895305	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7898330	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7906843	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs7913343	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7921721	1.00[CEU][hapmap];0.84[CHB][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8181426	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs912466	0.91[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs9420641	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs945123	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs955694	0.85[EUR][1000 genomes]
rs9633675	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9633699	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv831946	chr10:96055190-96226438	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10882460	KIF11	cis	cerebellum	SCAN
rs10882460	HELLS	cis	cerebellum	SCAN
rs10882460	FGFBP3	cis	cerebellum	SCAN
rs10882460	C19orf22	trans	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96188400-96213600	Weak transcription	Stomach Mucosa	stomach
2	chr10:96190800-96234600	Weak transcription	Osteobl	bone
3	chr10:96198400-96218200	Weak transcription	Aorta	Aorta
4	chr10:96199200-96215400	Weak transcription	Fetal Stomach	stomach
5	chr10:96199400-96212000	Weak transcription	Adipose Nuclei	Adipose
6	chr10:96199400-96215200	Weak transcription	Placenta	Placenta
7	chr10:96199400-96219600	Weak transcription	Pancreas	Pancrea
8	chr10:96200200-96219400	Weak transcription	Left Ventricle	heart
9	chr10:96201200-96219200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr10:96203000-96218600	Weak transcription	Ovary	ovary
11	chr10:96203000-96239600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr10:96203200-96215400	Weak transcription	Fetal Intestine Small	intestine
13	chr10:96203400-96212000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr10:96203400-96242800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr10:96203600-96218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr10:96203800-96217200	Weak transcription	HepG2	liver
17	chr10:96203800-96219600	Weak transcription	Brain Angular Gyrus	brain
18	chr10:96204000-96221000	Weak transcription	Liver	Liver
19	chr10:96204200-96212000	Weak transcription	Brain Anterior Caudate	brain
20	chr10:96204200-96213400	Weak transcription	A549	lung
21	chr10:96204200-96243400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr10:96206200-96218000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr10:96207600-96213200	Weak transcription	HUVEC	blood vessel
24	chr10:96209000-96218400	Weak transcription	Lung	lung
25	chr10:96209400-96213000	Strong transcription	HSMM	muscle
26	chr10:96209600-96219600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr10:96210200-96215800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:96210200-96248800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:96210400-96211600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr10:96210600-96215200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr10:96211200-96211600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:96211200-96211600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
33	chr10:96211200-96211600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
34	chr10:96211200-96212200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr10:96211200-96212200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr10:96211200-96212200	ZNF genes & repeats	Fetal Heart	heart
37	chr10:96211200-96212600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr10:96211200-96212800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
39	chr10:96211400-96211600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr10:96211400-96211600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
41	chr10:96211400-96211600	ZNF genes & repeats	Psoas Muscle	Psoas
42	chr10:96211400-96212200	ZNF genes & repeats	Brain Substantia Nigra	brain
43	chr10:96211400-96212400	ZNF genes & repeats	Fetal Lung	lung
44	chr10:96211400-96212600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
45	chr10:96211400-96218200	Weak transcription	Fetal Intestine Large	intestine

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