Variant report

Variant	rs10882486
Chromosome Location	chr10:96382128-96382129
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1018602	0.81[EUR][1000 genomes]
rs10786168	0.94[ASW][hapmap];0.92[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10786169	0.92[CEU][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10786170	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10786172	1.00[JPT][hapmap]
rs10882460	0.94[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs10882463	0.94[ASW][hapmap];0.91[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap]
rs10882470	0.86[MEX][hapmap]
rs10882474	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882477	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11187939	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11187940	0.92[JPT][hapmap]
rs11187944	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11187948	0.86[MEX][hapmap]
rs11187952	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs11187960	1.00[JPT][hapmap]
rs11187972	0.85[CEU][hapmap]
rs11187980	0.92[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs11188009	0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11188012	0.83[JPT][hapmap]
rs11188019	0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11188020	1.00[JPT][hapmap]
rs11188040	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs11638	0.92[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12218213	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs12218216	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs12219906	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs12220588	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs12221475	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs12570013	0.82[EUR][1000 genomes]
rs1326839	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1334595	1.00[JPT][hapmap]
rs1359262	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1359263	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs1409655	1.00[JPT][hapmap]
rs1854035	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1889486	0.86[MEX][hapmap]
rs1931757	0.83[JPT][hapmap]
rs1969815	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs1977288	1.00[JPT][hapmap]
rs1977291	0.83[JPT][hapmap]
rs1980741	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs2274096	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2274417	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs2281791	0.84[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2860821	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs2860840	1.00[JPT][hapmap]
rs3740358	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3758522	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3758523	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3781262	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4351744	0.92[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs4494250	0.94[JPT][hapmap]
rs4918402	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4918404	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4918409	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs4918412	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6583942	1.00[JPT][hapmap]
rs6583944	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs6583946	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs701885	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7075182	0.88[JPT][hapmap]
rs7078478	0.83[JPT][hapmap]
rs7078811	0.92[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7079934	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7083898	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs7087798	0.83[JPT][hapmap]
rs7092129	1.00[JPT][hapmap]
rs7100415	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7906843	0.88[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7913343	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs7921721	0.92[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs912466	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv517681	chr10:96343228-96387079	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10882486	C19orf22	trans	cerebellum	SCAN
rs10882486	KIF11	cis	cerebellum	SCAN
rs10882486	HELLS	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96370000-96382800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr10:96372600-96382200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr10:96372600-96382400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr10:96373200-96382400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:96373200-96383800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr10:96374000-96382200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr10:96374600-96386200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:96381600-96382800	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr10:96381800-96382400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr10:96382000-96382600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr10:96382000-96382600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:96382000-96382600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr10:96382000-96382600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:96382000-96382800	Weak transcription	Fetal Intestine Large	intestine
15	chr10:96382000-96383000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr10:96382000-96383000	Enhancers	H9 Cell Line	embryonic stem cell
17	chr10:96382000-96383800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr10:96382000-96383800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr10:96382000-96383800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr10:96382000-96384200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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