Variant report

Variant	rs1543640
Chromosome Location	chr9:21265259-21265260
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10113879	0.82[ASN][1000 genomes]
rs10114358	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10120675	0.82[ASN][1000 genomes]
rs10125010	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs10738591	0.82[ASN][1000 genomes]
rs10757208	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10757210	0.82[ASN][1000 genomes]
rs10811505	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10811519	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10811522	0.82[ASN][1000 genomes]
rs10811523	0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs10964878	0.94[JPT][hapmap]
rs10964920	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10964929	0.95[ASN][1000 genomes]
rs10964953	0.82[ASN][1000 genomes]
rs10964954	0.80[ASN][1000 genomes]
rs10964955	0.82[ASN][1000 genomes]
rs10964956	0.82[ASN][1000 genomes]
rs10964958	0.80[ASN][1000 genomes]
rs12552812	0.90[ASN][1000 genomes]
rs1330314	0.86[CHD][hapmap]
rs1330318	0.90[EUR][1000 genomes]
rs1330319	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1330320	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1330322	0.81[CEU][hapmap]
rs1330323	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1330324	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1330325	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1411437	0.97[ASN][1000 genomes]
rs1475547	0.80[ASN][1000 genomes]
rs1475548	0.82[ASN][1000 genomes]
rs1543874	0.82[ASN][1000 genomes]
rs1820315	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1831390	0.97[ASN][1000 genomes]
rs1831391	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1854700	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1952690	0.80[ASN][1000 genomes]
rs2094787	0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs2094788	0.84[CHD][hapmap]
rs3091288	1.00[JPT][hapmap]
rs3903111	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4634752	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4978056	0.97[ASN][1000 genomes]
rs67212517	0.82[ASN][1000 genomes]
rs7019617	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7019739	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7020867	0.80[ASN][1000 genomes]
rs7021699	0.80[ASN][1000 genomes]
rs7024738	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7031048	0.85[CHD][hapmap]
rs7037389	0.83[JPT][hapmap]
rs7037707	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7047351	0.82[ASN][1000 genomes]
rs7848803	0.90[ASN][1000 genomes]
rs7849623	1.00[JPT][hapmap]
rs7857863	0.89[ASN][1000 genomes]
rs7858766	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7866359	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs7868334	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs7872575	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9298814	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817218	chr9:20687769-21309177	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
3	nsv892734	chr9:21108817-21323089	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1035128	chr9:21196300-21269669	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv2761295	chr9:21258108-21281544	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3447912	chr9:21260652-21290903	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv430006	chr9:21262516-21280782	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1543640	KLHL9	cis	multi-tissue	Pritchard
rs1543640	KLHL9	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21264800-21265400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr9:21264800-21268600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr9:21265200-21265800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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