Variant report

Variant	rs10116540
Chromosome Location	chr9:21238152-21238153
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 137 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10117202	0.89[EUR][1000 genomes]
rs10120117	0.91[EUR][1000 genomes]
rs10122881	0.91[EUR][1000 genomes]
rs10124167	0.91[EUR][1000 genomes]
rs10124609	0.90[EUR][1000 genomes]
rs10738591	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10757199	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs10811489	0.82[EUR][1000 genomes]
rs10811497	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10811508	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10811509	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10811514	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10811527	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10811529	0.87[EUR][1000 genomes]
rs10964871	1.00[CEU][hapmap]
rs10964878	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10964884	1.00[CEU][hapmap]
rs10964885	1.00[CEU][hapmap]
rs10964896	1.00[CEU][hapmap]
rs10964918	0.86[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10964920	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs10964928	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10964929	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10964930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10964932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10964933	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10964934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10964943	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10964952	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10964957	0.93[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10964959	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10964961	0.91[EUR][1000 genomes]
rs1112783	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12345537	0.82[EUR][1000 genomes]
rs12551190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12552812	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12553763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12553910	0.84[EUR][1000 genomes]
rs12555631	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12555749	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1330312	0.91[EUR][1000 genomes]
rs1330314	0.93[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1330316	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1330317	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1330318	0.96[ASN][1000 genomes]
rs1330325	0.96[ASN][1000 genomes]
rs1411436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1424854	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap]
rs1590897	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1590898	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1820313	1.00[CEU][hapmap]
rs1831391	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs1834247	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1854700	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs1928854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928855	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1928856	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1952690	0.89[EUR][1000 genomes]
rs2007448	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2015345	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2098814	1.00[CEU][hapmap]
rs2225329	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28437205	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2939	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2988573	0.84[EUR][1000 genomes]
rs2988574	0.83[EUR][1000 genomes]
rs2990140	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs3750479	0.92[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap]
rs3758236	0.93[CEU][hapmap]
rs3855766	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3903111	0.96[ASN][1000 genomes]
rs3955236	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4007646	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4112794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568686	0.91[EUR][1000 genomes]
rs4582643	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs4628333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634752	0.82[YRI][hapmap]
rs4977682	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4977684	1.00[CEU][hapmap]
rs4977714	0.89[EUR][1000 genomes]
rs4978068	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4978069	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56035072	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57122438	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57146220	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57371737	0.84[EUR][1000 genomes]
rs583396	0.84[EUR][1000 genomes]
rs596180	0.86[CEU][hapmap];0.81[GIH][hapmap]
rs597440	0.82[EUR][1000 genomes]
rs604762	0.86[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs612966	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs614541	0.93[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs618507	0.85[EUR][1000 genomes]
rs637700	0.84[EUR][1000 genomes]
rs637949	0.86[CEU][hapmap];0.81[GIH][hapmap]
rs6475510	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs660675	0.81[EUR][1000 genomes]
rs667214	0.83[EUR][1000 genomes]
rs667635	0.83[EUR][1000 genomes]
rs681680	0.84[EUR][1000 genomes]
rs7019617	1.00[CEU][hapmap]
rs7019739	1.00[CEU][hapmap]
rs7022016	0.82[EUR][1000 genomes]
rs7030705	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs7031048	0.93[CEU][hapmap];0.95[TSI][hapmap]
rs7033839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs7035639	1.00[CEU][hapmap]
rs7037147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7037707	0.95[ASN][1000 genomes]
rs7041635	1.00[CEU][hapmap]
rs7043560	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7046898	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7047240	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7047351	0.87[EUR][1000 genomes]
rs7047805	0.93[CEU][hapmap]
rs7047811	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap]
rs73418252	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs768848	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs768849	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7848803	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7849623	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7849862	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs7852809	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7854247	1.00[CEU][hapmap]
rs7856345	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7857863	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7866359	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7866640	0.89[EUR][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	nsv1032466	chr9:21052069-21243756	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv540084	chr9:21052069-21243756	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	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
6	nsv892735	chr9:21157373-21242161	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv968599	chr9:21166047-21239960	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	10 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10116540	KLHL9	cis	lymphoblastoid	seeQTL
rs10116540	KLHL9	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21236200-21244600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:21236400-21239800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr9:21236400-21244600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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