Variant report

Variant	rs659023
Chromosome Location	chr11:85824859-85824860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85823091..85825263-chr11:85834744..85836262,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10751134	0.91[JPT][hapmap]
rs10792830	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10792831	0.86[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs10792832	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10898438	0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10898439	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs1237999	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1898895	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2508692	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2508696	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs3016786	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs3851178	0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3851179	0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs471470	0.91[ASN][1000 genomes]
rs472486	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs474479	0.90[ASN][1000 genomes]
rs475639	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap]
rs484154	0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs493254	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4944560	0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs497816	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs519961	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs526904	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs532470	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs541458	0.84[GIH][hapmap]
rs542126	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs543293	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs545592	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs561646	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs561655	0.83[CHB][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap]
rs566975	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs572979	0.85[ASN][1000 genomes]
rs573167	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs580887	0.96[ASN][1000 genomes]
rs583162	0.94[ASN][1000 genomes]
rs586274	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs597446	0.84[LWK][hapmap]
rs602222	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs609903	0.86[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs613222	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs618001	0.82[LWK][hapmap]
rs629343	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.94[ASN][1000 genomes]
rs631611	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs645293	0.90[ASN][1000 genomes]
rs645299	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs666682	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap]
rs669813	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs676733	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap]
rs677909	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs682928	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs683494	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs694011	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs7113976	0.83[CHB][hapmap]
rs7114331	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7114401	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7129687	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7941541	0.91[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]
rs867611	0.89[CHB][hapmap];0.94[JPT][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	nsv1050948	chr11:85756325-85968665	Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv541117	chr11:85756325-85968665	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs659023	GRM5	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85813600-85826600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:85824800-85825400	Enhancers	K562	blood
3	chr11:85824800-85837600	Weak transcription	Brain Angular Gyrus	brain

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