Variant report

Variant	rs6475527
Chromosome Location	chr9:21265617-21265618
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10116615	0.90[EUR][1000 genomes]
rs10116936	0.92[ASN][1000 genomes]
rs10117202	0.81[ASN][1000 genomes]
rs10117677	0.92[EUR][1000 genomes]
rs10120117	0.81[ASN][1000 genomes]
rs10122881	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10124167	0.82[ASN][1000 genomes]
rs10757212	0.92[EUR][1000 genomes]
rs10757213	0.92[EUR][1000 genomes]
rs10811522	0.91[EUR][1000 genomes]
rs10811523	0.91[EUR][1000 genomes]
rs10811527	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10964932	0.83[AMR][1000 genomes]
rs10964933	0.83[AMR][1000 genomes]
rs10964934	0.83[AMR][1000 genomes]
rs10964943	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10964952	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10964953	0.91[EUR][1000 genomes]
rs10964954	0.90[EUR][1000 genomes]
rs10964955	0.91[EUR][1000 genomes]
rs10964956	0.91[EUR][1000 genomes]
rs10964957	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10964958	0.91[EUR][1000 genomes]
rs10964959	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10964960	0.93[EUR][1000 genomes]
rs10964961	0.80[ASN][1000 genomes]
rs10964966	0.92[EUR][1000 genomes]
rs1112783	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12237982	0.92[EUR][1000 genomes]
rs1224392	0.84[EUR][1000 genomes]
rs12551190	0.83[AMR][1000 genomes]
rs12683349	0.92[EUR][1000 genomes]
rs1330311	0.91[EUR][1000 genomes]
rs1330312	0.82[ASN][1000 genomes]
rs1330313	0.92[EUR][1000 genomes]
rs1330317	0.88[AMR][1000 genomes]
rs1360286	0.92[EUR][1000 genomes]
rs1411436	0.83[AMR][1000 genomes]
rs1411437	0.91[EUR][1000 genomes]
rs1467734	0.92[EUR][1000 genomes]
rs1467735	0.92[EUR][1000 genomes]
rs1467736	0.92[EUR][1000 genomes]
rs1475547	0.91[EUR][1000 genomes]
rs1475548	0.91[EUR][1000 genomes]
rs1543874	0.91[EUR][1000 genomes]
rs1590897	0.92[ASN][1000 genomes]
rs1590898	0.85[AMR][1000 genomes]
rs1831390	0.91[EUR][1000 genomes]
rs2094787	0.91[EUR][1000 genomes]
rs2094788	0.91[EUR][1000 genomes]
rs2225329	0.85[AMR][1000 genomes]
rs2480927	0.84[EUR][1000 genomes]
rs28437205	0.84[AMR][1000 genomes]
rs4406500	0.91[EUR][1000 genomes]
rs4568686	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4977714	0.84[ASN][1000 genomes]
rs4978056	0.91[EUR][1000 genomes]
rs4978069	0.85[AMR][1000 genomes]
rs4978092	0.91[EUR][1000 genomes]
rs4978093	0.92[EUR][1000 genomes]
rs4978097	0.91[EUR][1000 genomes]
rs57122438	0.82[AMR][1000 genomes]
rs57146220	0.82[AMR][1000 genomes]
rs600118	0.90[EUR][1000 genomes]
rs616873	0.90[EUR][1000 genomes]
rs667069	0.91[EUR][1000 genomes]
rs67212517	0.91[EUR][1000 genomes]
rs7020867	0.91[EUR][1000 genomes]
rs7021699	0.90[EUR][1000 genomes]
rs7032044	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7035600	0.91[EUR][1000 genomes]
rs7035669	0.92[EUR][1000 genomes]
rs73418252	0.85[AMR][1000 genomes]
rs7849902	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7853081	0.92[EUR][1000 genomes]
rs7862940	0.92[EUR][1000 genomes]
rs7866640	0.82[ASN][1000 genomes]
rs7872479	0.91[EUR][1000 genomes]
rs8729	0.91[EUR][1000 genomes]

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
rs6475527	KLHL9	cis	multi-tissue	Pritchard
rs6475527	KLHL9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21264800-21268600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr9:21265200-21265800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:21265400-21266800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr9:21265600-21265800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:21265600-21266000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:21265600-21266000	Enhancers	Fetal Thymus	thymus
7	chr9:21265600-21267200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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