Variant report

Variant	rs7035600
Chromosome Location	chr9:21310833-21310834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10113879	0.97[ASN][1000 genomes]
rs10116615	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117677	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10119678	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[MEX][hapmap]
rs10120675	0.97[ASN][1000 genomes]
rs10125010	0.94[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs10738591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10757208	0.96[ASN][1000 genomes]
rs10757210	0.97[ASN][1000 genomes]
rs10757212	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10757213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[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];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811523	0.80[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10811529	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10964953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10964954	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10964955	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10964956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10964958	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10964960	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10964966	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12237982	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1224392	0.91[EUR][1000 genomes]
rs12553910	0.80[ASN][1000 genomes]
rs12683349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330311	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1330314	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1330323	0.96[ASN][1000 genomes]
rs1330324	0.96[ASN][1000 genomes]
rs1360286	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411437	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1467734	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1467735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1467736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1475547	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1475548	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1543874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1820314	0.89[CEU][hapmap]
rs1820315	0.82[YRI][hapmap]
rs1831390	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1831391	0.80[YRI][hapmap]
rs1952690	0.82[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];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.95[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];0.87[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2480927	0.91[EUR][1000 genomes]
rs3758236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4406500	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4978056	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4978092	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4978093	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4978097	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600118	0.97[EUR][1000 genomes]
rs616873	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6475527	0.91[EUR][1000 genomes]
rs667069	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67212517	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7019617	0.81[YRI][hapmap]
rs7020867	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7021699	0.93[AMR][1000 genomes];0.94[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];0.87[MEX][hapmap]
rs7032044	0.93[EUR][1000 genomes]
rs7035669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849623	0.83[MEX][hapmap]
rs7849902	0.92[EUR][1000 genomes]
rs7853081	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7858766	0.96[ASN][1000 genomes]
rs7862940	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7868334	0.94[CEU][hapmap];0.80[CHD][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs7872479	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7872575	0.96[ASN][1000 genomes]
rs8729	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9298814	0.94[CEU][hapmap];0.82[YRI][hapmap]

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	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
3	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
rs7035600	KLHL9	Cis_1M	lymphoblastoid	RTeQTL
rs7035600	KLHL9	cis	lymphoblastoid	seeQTL
rs7035600	KLHL9	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21309000-21312000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:21309800-21322600	Weak transcription	Brain Substantia Nigra	brain
3	chr9:21310400-21311800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:21310800-21311400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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