Variant report

Variant	rs4978097
Chromosome Location	chr9:21294921-21294922
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10113879	0.97[ASN][1000 genomes]
rs10116615	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117677	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10119678	0.82[CEU][hapmap];0.82[CHB][hapmap];0.87[MEX][hapmap]
rs10120675	0.97[ASN][1000 genomes]
rs10125010	0.94[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs10738591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10757208	0.96[ASN][1000 genomes]
rs10757210	0.97[ASN][1000 genomes]
rs10757212	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10757213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10811505	0.94[CEU][hapmap]
rs10811519	0.96[ASN][1000 genomes]
rs10811522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811523	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811529	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10964878	0.83[MEX][hapmap]
rs10964953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10964954	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10964955	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10964956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10964958	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10964960	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10964966	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12237982	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1224392	0.88[EUR][1000 genomes]
rs12553910	0.80[ASN][1000 genomes]
rs12683349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330311	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330314	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1330323	0.96[ASN][1000 genomes]
rs1330324	0.96[ASN][1000 genomes]
rs1360286	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411437	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1467734	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1467735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1467736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1475547	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1475548	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1543874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1820314	0.89[CEU][hapmap]
rs1831390	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1952690	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2094787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2094788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2480927	0.88[EUR][1000 genomes]
rs3758236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4406500	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4568686	0.80[AFR][1000 genomes]
rs4978056	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4978092	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4978093	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600118	0.94[EUR][1000 genomes]
rs616873	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6475527	0.91[EUR][1000 genomes]
rs667069	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67212517	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7020867	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7021699	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7031048	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs7032044	0.98[EUR][1000 genomes]
rs7035600	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035669	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849623	0.87[MEX][hapmap]
rs7849902	0.97[EUR][1000 genomes]
rs7853081	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7858766	0.96[ASN][1000 genomes]
rs7862940	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7868334	0.94[CEU][hapmap];0.80[CHD][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs7872479	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7872575	0.96[ASN][1000 genomes]
rs8729	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9298814	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv2757325	chr9:21281544-21303689	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
5	esv2759679	chr9:21281544-21303689	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
6	esv3693022	chr9:21285389-21306318	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
7	nsv438097	chr9:21285389-21306318	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
8	nsv613757	chr9:21289923-21316649	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4978097	KLHL9	cis	multi-tissue	Pritchard
rs4978097	KLHL9	cis	lymphoblastoid	seeQTL
rs4978097	KLHL9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21293600-21295200	Enhancers	HMEC	breast
2	chr9:21293800-21295400	Enhancers	Hela-S3	cervix
3	chr9:21294000-21295400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:21294200-21295000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:21294200-21295000	Enhancers	NHEK	skin
6	chr9:21294200-21295200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:21294400-21295200	Flanking Active TSS	GM12878-XiMat	blood
8	chr9:21294400-21295400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:21294400-21296800	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr9:21294400-21297000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:21294600-21295600	Bivalent Enhancer	Primary B cells from cord blood	blood
12	chr9:21294800-21296600	Enhancers	Primary hematopoietic stem cells	blood
13	chr9:21294800-21296600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr9:21294800-21296800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr9:21294800-21296800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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