Variant report

Variant	rs10964878
Chromosome Location	chr9:21171267-21171268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:21171078-21171278	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
IFNA21	TF binding region

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10116540	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10124609	0.84[EUR][1000 genomes]
rs10125010	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap]
rs10738591	1.00[CEU][hapmap]
rs10757199	1.00[CEU][hapmap]
rs10811489	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10811497	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10811505	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs10811508	0.86[EUR][1000 genomes]
rs10811509	0.85[EUR][1000 genomes]
rs10811523	0.85[GIH][hapmap];0.83[MEX][hapmap]
rs10964871	1.00[CEU][hapmap]
rs10964884	1.00[CEU][hapmap];0.81[YRI][hapmap]
rs10964885	1.00[CEU][hapmap]
rs10964896	1.00[CEU][hapmap]
rs10964918	0.86[CEU][hapmap]
rs10964920	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs10964930	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs10964932	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs10964934	1.00[CEU][hapmap]
rs10964957	0.93[CEU][hapmap];0.94[TSI][hapmap]
rs12345537	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12551190	1.00[CEU][hapmap];0.84[YRI][hapmap]
rs12553763	1.00[CEU][hapmap]
rs12555631	1.00[CEU][hapmap]
rs12555749	0.83[EUR][1000 genomes]
rs1330314	0.93[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs1411436	1.00[CEU][hapmap]
rs1424854	1.00[CEU][hapmap]
rs1820313	1.00[CEU][hapmap]
rs1820315	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1831391	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs1834247	1.00[CEU][hapmap]
rs1854700	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1928854	1.00[CEU][hapmap]
rs2007448	0.86[EUR][1000 genomes]
rs2015345	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2032996	0.82[JPT][hapmap]
rs2094787	0.85[GIH][hapmap];0.95[MEX][hapmap]
rs2094788	0.85[GIH][hapmap];0.95[MEX][hapmap]
rs2098814	1.00[CEU][hapmap]
rs2383182	0.82[YRI][hapmap]
rs2939	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs2990140	0.91[CEU][hapmap]
rs3091288	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3750479	1.00[CEU][hapmap]
rs3758236	0.93[CEU][hapmap]
rs3855766	0.82[EUR][1000 genomes]
rs3955236	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4007646	0.85[EUR][1000 genomes]
rs4582643	0.93[CEU][hapmap];0.95[TSI][hapmap]
rs4628333	1.00[CEU][hapmap]
rs4634752	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4977682	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs4977684	1.00[CEU][hapmap]
rs56035072	0.85[EUR][1000 genomes]
rs596180	0.86[CEU][hapmap]
rs604762	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs612966	0.93[CEU][hapmap]
rs614541	0.93[CEU][hapmap];0.85[TSI][hapmap]
rs637949	0.86[CEU][hapmap]
rs6475510	0.85[EUR][1000 genomes]
rs7019617	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs7019739	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7022016	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7025904	0.85[EUR][1000 genomes]
rs7030705	1.00[CEU][hapmap]
rs7031048	0.93[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7033839	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7035639	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs7037147	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7041635	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs7043560	0.86[EUR][1000 genomes]
rs7046898	0.86[EUR][1000 genomes]
rs7047240	0.86[EUR][1000 genomes]
rs7047351	0.83[EUR][1000 genomes]
rs7047805	0.93[CEU][hapmap];0.81[YRI][hapmap]
rs7047811	1.00[CEU][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap]
rs73416528	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs768848	0.86[EUR][1000 genomes]
rs768849	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7849623	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap]
rs7849862	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7852323	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7852809	0.86[EUR][1000 genomes]
rs7854247	1.00[CEU][hapmap]
rs7856345	0.84[EUR][1000 genomes]
rs7866359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs7868334	0.95[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap]
rs8729	0.83[MEX][hapmap]
rs9298814	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs980639	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv466293	chr9:21029330-21199680	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv613752	chr9:21029330-21199680	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	nsv613755	chr9:21170364-21216028	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1016978	chr9:21171267-21214877	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10964878	KLHL9	cis	lymphoblastoid	seeQTL
rs10964878	KLHL9	cis	multi-tissue	Pritchard

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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