Variant report

Variant	rs10120117
Chromosome Location	chr9:21295318-21295319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 132 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10116540	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs10116936	0.88[ASN][1000 genomes]
rs10117202	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10122881	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10124167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10124609	0.82[EUR][1000 genomes]
rs10738591	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10757199	0.93[CEU][hapmap]
rs10811497	0.93[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10811508	0.84[EUR][1000 genomes]
rs10811509	0.85[EUR][1000 genomes]
rs10811514	0.89[EUR][1000 genomes]
rs10811527	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811529	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10964871	0.93[CEU][hapmap]
rs10964878	0.93[CEU][hapmap];0.95[TSI][hapmap]
rs10964884	0.92[CEU][hapmap]
rs10964885	0.93[CEU][hapmap]
rs10964896	0.93[CEU][hapmap]
rs10964918	0.89[EUR][1000 genomes]
rs10964920	0.93[CEU][hapmap]
rs10964928	0.91[EUR][1000 genomes]
rs10964929	0.87[EUR][1000 genomes]
rs10964930	0.93[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10964932	0.93[CEU][hapmap];0.91[LWK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10964933	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10964934	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10964943	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10964952	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10964957	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10964959	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10964961	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1112783	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12551190	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12552812	0.88[EUR][1000 genomes]
rs12553763	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12553910	0.92[EUR][1000 genomes]
rs12555631	0.93[CEU][hapmap]
rs12555749	0.86[EUR][1000 genomes]
rs1330312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1330313	0.81[CEU][hapmap]
rs1330314	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1330317	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1411436	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1424854	1.00[CEU][hapmap]
rs1590897	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1590898	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1820313	0.93[CEU][hapmap]
rs1831391	0.93[CEU][hapmap]
rs1834247	0.93[CEU][hapmap]
rs1854700	0.93[CEU][hapmap]
rs1928854	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs1928855	0.90[EUR][1000 genomes]
rs1928856	0.89[EUR][1000 genomes]
rs1952690	0.98[EUR][1000 genomes]
rs2007448	0.84[EUR][1000 genomes]
rs2015345	0.80[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap]
rs2098814	0.93[CEU][hapmap]
rs2225329	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28437205	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2939	0.80[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs2988573	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2988574	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2990140	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[YRI][hapmap];0.91[EUR][1000 genomes]
rs2990141	0.84[CEU][hapmap]
rs3750479	0.93[CEU][hapmap]
rs3758236	1.00[CEU][hapmap]
rs3955236	0.93[CEU][hapmap]
rs4007646	0.83[EUR][1000 genomes]
rs4112794	0.91[EUR][1000 genomes]
rs4568686	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4582643	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4628333	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs4977682	0.93[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs4977684	0.93[CEU][hapmap]
rs4977714	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4978069	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56035072	0.85[EUR][1000 genomes]
rs57122438	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57146220	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57371737	0.93[EUR][1000 genomes]
rs583396	0.93[EUR][1000 genomes]
rs596180	0.93[CEU][hapmap];0.81[GIH][hapmap]
rs597440	0.89[EUR][1000 genomes]
rs604762	1.00[ASW][hapmap];0.93[CEU][hapmap];0.94[CHB][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs612966	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs614541	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs618507	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs637700	0.93[EUR][1000 genomes]
rs637949	0.93[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs6475510	0.83[EUR][1000 genomes]
rs6475527	0.81[ASN][1000 genomes]
rs653778	0.85[EUR][1000 genomes]
rs660675	0.89[EUR][1000 genomes]
rs667214	0.91[EUR][1000 genomes]
rs667635	0.91[EUR][1000 genomes]
rs681680	0.93[EUR][1000 genomes]
rs7019617	0.92[CEU][hapmap]
rs7019739	0.93[CEU][hapmap]
rs7030705	0.93[CEU][hapmap]
rs7031048	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7032044	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7033839	0.93[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs7035639	0.93[CEU][hapmap]
rs7037147	0.93[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs7041635	0.93[CEU][hapmap]
rs7043560	0.84[EUR][1000 genomes]
rs7046898	0.84[EUR][1000 genomes]
rs7047240	0.84[EUR][1000 genomes]
rs7047805	0.86[CEU][hapmap]
rs7047811	0.93[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap]
rs73418252	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs768848	0.84[EUR][1000 genomes]
rs768849	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs7848803	0.89[EUR][1000 genomes]
rs7849623	0.93[CEU][hapmap];0.95[TSI][hapmap]
rs7849862	0.93[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs7849902	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7852809	0.84[EUR][1000 genomes]
rs7854247	0.93[CEU][hapmap]
rs7856345	0.82[EUR][1000 genomes]
rs7857863	0.88[EUR][1000 genomes]
rs7866359	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs7866640	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10120117	KLHL9	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21293800-21295400	Enhancers	Hela-S3	cervix
2	chr9:21294000-21295400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:21294400-21295400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:21294400-21296800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr9:21294400-21297000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:21294600-21295600	Bivalent Enhancer	Primary B cells from cord blood	blood
7	chr9:21294800-21296600	Enhancers	Primary hematopoietic stem cells	blood
8	chr9:21294800-21296600	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr9:21294800-21296800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr9:21294800-21296800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr9:21295000-21296400	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr9:21295200-21295800	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr9:21295200-21296000	Enhancers	GM12878-XiMat	blood

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