Variant report

Variant	rs11226828
Chromosome Location	chr11:105568411-105568412
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1037090	0.85[CEU][hapmap]
rs10502059	0.90[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs10502060	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]
rs10791764	0.90[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[ASN][1000 genomes]
rs10791767	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10895851	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10895852	0.84[ASN][1000 genomes]
rs10895856	0.89[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs10895857	1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10895859	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10895860	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895864	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10895868	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10895870	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10895871	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10895872	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11226818	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11226819	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11226820	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11226825	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11226827	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11226834	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11226835	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11601239	0.91[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs11601808	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11606220	0.89[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs12286810	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12290919	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12291501	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12294986	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12417624	1.00[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12575513	0.84[ASN][1000 genomes]
rs12575516	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12576615	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12790329	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1373926	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1445599	0.83[ASN][1000 genomes]
rs1445600	0.83[ASN][1000 genomes]
rs1445607	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1445610	0.82[ASN][1000 genomes]
rs1445613	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs1445617	0.85[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs1445618	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1445619	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1445622	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1542162	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1822982	0.84[ASN][1000 genomes]
rs1822985	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1822989	0.85[CEU][hapmap]
rs1822993	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1838668	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938963	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1938964	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1938965	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1938970	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1938971	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1942966	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1942978	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1942979	0.82[ASN][1000 genomes]
rs1954762	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1964460	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2028816	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2121061	0.84[ASN][1000 genomes]
rs2155043	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4480512	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4755107	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs499945	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs519193	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs521893	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs556609	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs590928	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs627041	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs632100	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs638099	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs639076	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs687502	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7102566	0.90[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs7106983	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7114305	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7115043	0.84[ASN][1000 genomes]
rs7122727	0.90[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.84[ASN][1000 genomes]
rs7129054	0.82[ASN][1000 genomes]
rs7130156	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7926520	1.00[CEU][hapmap];0.98[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7928594	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7931588	0.96[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7932892	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7944207	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7951215	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs977516	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs994575	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11226828	GRIA4	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105561400-105586200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:105564800-105569400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:105564800-105569600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr11:105566600-105569600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:105567000-105596600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:105567800-105568600	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr11:105568000-105568600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr11:105568000-105568600	Enhancers	H9 Cell Line	embryonic stem cell
9	chr11:105568000-105568600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr11:105568000-105568600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr11:105568200-105568600	Enhancers	Brain Hippocampus Middle	brain
12	chr11:105568200-105570200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr11:105568200-105571600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:105568200-105572000	Enhancers	Brain Substantia Nigra	brain
15	chr11:105568400-105570400	Enhancers	Cortex derived primary cultured neurospheres	brain

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