Variant report

Variant	rs604762
Chromosome Location	chr9:21354180-21354181
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	STAT3	chr9:21353876-21354230	MCF10A-Er-Src	breast:	n/a	n/a
2	SETDB1	chr9:21354154-21354615	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
IFNA6	TF binding region

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10116540	0.86[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10117202	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10120117	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10122881	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10124167	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10738591	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10757199	0.81[CEU][hapmap]
rs10811497	0.86[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs10811514	0.82[EUR][1000 genomes]
rs10811527	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10811529	0.93[EUR][1000 genomes]
rs10964871	0.81[CEU][hapmap]
rs10964878	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs10964884	0.80[CEU][hapmap]
rs10964885	0.81[CEU][hapmap]
rs10964896	0.81[CEU][hapmap]
rs10964918	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs10964920	0.81[CEU][hapmap]
rs10964928	0.84[EUR][1000 genomes]
rs10964929	0.80[EUR][1000 genomes]
rs10964930	0.86[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs10964932	0.86[CEU][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10964933	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10964934	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10964943	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10964952	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10964957	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10964959	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10964961	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1112783	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12551190	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12552812	0.81[EUR][1000 genomes]
rs12553763	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs12553910	0.89[EUR][1000 genomes]
rs12555631	0.81[CEU][hapmap]
rs1330312	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1330314	0.93[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs1330317	0.85[AMR][1000 genomes]
rs1411436	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1424854	0.86[CEU][hapmap]
rs1590897	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1590898	0.82[AMR][1000 genomes]
rs1820313	0.81[CEU][hapmap]
rs1831391	0.80[CEU][hapmap]
rs1834247	0.81[CEU][hapmap]
rs1854700	0.81[CEU][hapmap]
rs1928854	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1928855	0.83[EUR][1000 genomes]
rs1928856	0.82[EUR][1000 genomes]
rs1952690	0.90[EUR][1000 genomes]
rs2015345	0.80[ASW][hapmap];0.86[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs2098814	0.81[CEU][hapmap]
rs2225329	0.82[AMR][1000 genomes]
rs28437205	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2939	0.80[ASW][hapmap];0.86[CEU][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs2988573	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2988574	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2990140	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2990141	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs3750479	0.86[CEU][hapmap]
rs3758236	0.87[CEU][hapmap]
rs3955236	0.81[CEU][hapmap]
rs4112794	0.84[EUR][1000 genomes]
rs4568686	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4582643	0.93[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4628333	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs4977682	0.86[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs4977684	0.81[CEU][hapmap]
rs4977714	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4978069	0.82[AMR][1000 genomes]
rs4978114	0.85[CEU][hapmap]
rs57122438	0.84[EUR][1000 genomes]
rs57146220	0.84[EUR][1000 genomes]
rs57371737	0.96[EUR][1000 genomes]
rs583396	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596180	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap]
rs597440	0.99[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs612966	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs614541	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs617881	0.80[EUR][1000 genomes]
rs618507	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs637700	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs637949	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap]
rs647167	0.80[EUR][1000 genomes]
rs653778	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs660675	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs662831	0.80[EUR][1000 genomes]
rs667214	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs667635	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs674189	0.80[EUR][1000 genomes]
rs681680	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7019617	0.84[CEU][hapmap]
rs7019739	0.81[CEU][hapmap]
rs7030705	0.81[CEU][hapmap]
rs7031048	0.93[CEU][hapmap];0.90[TSI][hapmap]
rs7032044	0.84[AMR][1000 genomes]
rs7033839	0.86[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap]
rs7035639	0.81[CEU][hapmap]
rs7037147	0.86[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs7041635	0.81[CEU][hapmap]
rs7047811	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs73418252	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs768849	0.81[CEU][hapmap]
rs7848803	0.82[EUR][1000 genomes]
rs7849623	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs7849862	0.86[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs7849902	0.84[AMR][1000 genomes]
rs7854247	0.80[CEU][hapmap]
rs7857863	0.81[EUR][1000 genomes]
rs7866359	0.81[CEU][hapmap]
rs7866640	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv892736	chr9:21327141-21391698	Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv892737	chr9:21352862-21408824	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs604762	KLHL9	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21353800-21357000	Weak transcription	GM12878-XiMat	blood

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