Variant report

Variant	rs543293
Chromosome Location	chr11:85820077-85820078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85812308..85815576-chr11:85816844..85820250,5	K562	blood:
2	chr11:85752580..85755769-chr11:85817812..85820593,3	K562	blood:
3	chr11:85818918..85820717-chr11:85851486..85854070,2	K562	blood:
4	chr11:85816871..85820639-chr11:85825942..85829677,4	K562	blood:
5	chr11:85778125..85779781-chr11:85819659..85821681,2	K562	blood:
6	chr11:85752580..85754495-chr11:85817812..85820593,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10751134	0.87[ASW][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap]
rs10792830	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10792831	0.86[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]
rs10792832	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10898438	0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs10898439	0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs1237999	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1898895	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2458493	0.82[YRI][hapmap]
rs2458496	0.82[YRI][hapmap]
rs2458500	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs2508692	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2508696	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2509608	1.00[YRI][hapmap]
rs2509609	0.80[AFR][1000 genomes]
rs3016786	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs3851178	0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs3851179	0.87[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs471470	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs472486	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs474479	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs475639	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs480781	0.85[AFR][1000 genomes]
rs484154	0.81[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs493254	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4944560	0.91[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs497816	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs519961	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs526904	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs527162	1.00[ASW][hapmap];0.94[LWK][hapmap];0.82[YRI][hapmap]
rs532470	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs536841	0.86[ASW][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.82[YRI][hapmap]
rs542126	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545592	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs561646	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs561655	0.80[CEU][hapmap];0.83[CHB][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs566975	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs572979	0.82[ASN][1000 genomes]
rs573167	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs580887	0.90[ASN][1000 genomes]
rs583162	0.91[ASN][1000 genomes]
rs586274	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588076	0.89[LWK][hapmap]
rs592297	1.00[ASW][hapmap];0.94[LWK][hapmap];0.82[YRI][hapmap]
rs600743	0.82[YRI][hapmap]
rs602222	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs609903	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs613222	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs629343	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs631611	0.96[ASN][1000 genomes]
rs635168	0.80[AFR][1000 genomes]
rs637304	0.82[YRI][hapmap]
rs645293	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs645299	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs659023	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs666682	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs669813	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs676733	0.87[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap]
rs677909	1.00[ASW][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.82[YRI][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]
rs7110631	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7113976	0.83[CHB][hapmap]
rs7114331	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs7114401	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7129687	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7941541	1.00[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs867611	0.89[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3332891	chr11:85819854-85823752	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs543293	GRM5	cis	cerebellum	SCAN

Chromatin state (count:5 , 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	chr11:85818400-85820200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:85819800-85820400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:85819800-85820800	Flanking Active TSS	K562	blood
5	chr11:85820000-85820600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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