Variant report

Variant	rs7872575
Chromosome Location	chr9:21267134-21267135
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10113879	0.92[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10114358	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10116615	0.96[ASN][1000 genomes]
rs10117677	0.80[JPT][hapmap]
rs10120675	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10738591	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10757208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10757210	0.99[ASN][1000 genomes]
rs10757212	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10757213	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10811519	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10811522	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10811523	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10811529	0.96[ASN][1000 genomes]
rs10964953	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10964954	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10964955	0.99[ASN][1000 genomes]
rs10964956	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10964958	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10964960	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10964966	0.94[ASN][1000 genomes]
rs12683349	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1330311	0.89[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1330313	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1330314	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1330318	0.87[EUR][1000 genomes]
rs1330319	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1330320	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1330322	0.83[CEU][hapmap]
rs1330323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330324	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330325	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1360286	0.96[ASN][1000 genomes]
rs1411437	0.81[ASN][1000 genomes]
rs1467734	0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs1467735	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1467736	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1475547	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1475548	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1543640	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1543874	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1831390	0.81[ASN][1000 genomes]
rs1952690	0.98[ASN][1000 genomes]
rs2094787	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2094788	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3758236	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3903111	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4406500	0.97[ASN][1000 genomes]
rs4978056	0.81[ASN][1000 genomes]
rs4978092	0.97[ASN][1000 genomes]
rs4978093	0.96[ASN][1000 genomes]
rs4978097	0.96[ASN][1000 genomes]
rs67212517	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7020867	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7021699	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7024738	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7031048	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7035600	0.96[ASN][1000 genomes]
rs7035669	0.96[ASN][1000 genomes]
rs7037707	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7853081	0.93[ASN][1000 genomes]
rs7858766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7862940	0.94[ASN][1000 genomes]
rs8729	0.82[CHB][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7872575	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	chr9:21265600-21267200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:21266800-21267200	Enhancers	GM12878-XiMat	blood
4	chr9:21266800-21267400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:21266800-21267600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
6	chr9:21266800-21268600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr9:21267000-21267400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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