Variant report

Variant	rs10502060
Chromosome Location	chr11:105524546-105524547
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1037090	0.80[CHB][hapmap];0.84[EUR][1000 genomes]
rs10502059	0.96[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10791764	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];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10791767	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs10895847	0.85[AFR][1000 genomes]
rs10895851	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895852	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10895853	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10895856	0.80[CHB][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap]
rs10895857	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs10895859	0.82[ASN][1000 genomes]
rs10895860	0.88[ASW][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs10895870	0.80[CHB][hapmap]
rs10895871	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11226818	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11226819	0.95[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11226820	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11226822	0.84[EUR][1000 genomes]
rs11226827	0.80[CHB][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs11226828	0.90[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs11601239	0.83[CHB][hapmap]
rs11606220	0.82[CEU][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12286810	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12290919	0.80[CHB][hapmap]
rs12294986	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12417624	0.80[CHB][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs12575513	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12575516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12576615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12790329	0.82[ASN][1000 genomes]
rs1373926	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1445599	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1445600	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1445607	0.80[CHB][hapmap]
rs1445610	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1445613	0.82[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1445617	0.80[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs1445619	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1542162	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1822982	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1822985	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1822989	0.80[CHB][hapmap];0.87[EUR][1000 genomes]
rs1822993	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1838668	0.94[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs1938971	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1942966	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1942978	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1942979	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1964460	0.81[ASN][1000 genomes]
rs2121061	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3170	0.80[CHB][hapmap]
rs4301761	0.93[YRI][hapmap];0.85[AFR][1000 genomes]
rs4480512	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4755106	0.83[ASN][1000 genomes]
rs4755107	0.82[CEU][hapmap];0.80[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5006890	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs519193	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs556609	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs58045982	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs590928	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs632100	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs638099	0.94[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs639076	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6591137	0.93[LWK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs7102566	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7114305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7115043	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7122727	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7129054	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7130156	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs722295	0.92[CEU][hapmap];0.84[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7926520	0.80[CHB][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap]
rs7928594	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs7931588	0.80[CHB][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs7944207	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs7951215	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs977516	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs994575	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]

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	nsv1053687	chr11:105513034-105595722	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv832256	chr11:105516593-105689326	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10502060	GRIA4	cis	cerebellum	SCAN
rs10502060	DDI1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105517400-105525400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:105518000-105524600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr11:105522800-105526400	Weak transcription	Brain Angular Gyrus	brain
4	chr11:105524200-105556800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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