Variant report

Variant	rs9489379
Chromosome Location	chr6:118739604-118739605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10080340	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10155773	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs10214801	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10457339	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs10457340	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11153749	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11153751	1.00[EUR][1000 genomes]
rs11153762	0.80[AFR][1000 genomes]
rs12191529	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12191962	1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs12198458	0.85[EUR][1000 genomes]
rs12199189	1.00[EUR][1000 genomes]
rs12199190	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12199786	1.00[EUR][1000 genomes]
rs12202832	1.00[EUR][1000 genomes]
rs12202932	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12203556	1.00[EUR][1000 genomes]
rs12206369	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12206459	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12207121	1.00[EUR][1000 genomes]
rs12207554	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12209500	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12212089	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12215706	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13328242	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs13437148	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs13437314	0.80[AFR][1000 genomes]
rs4374854	0.83[GIH][hapmap]
rs6903291	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6903632	1.00[ASW][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6904070	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6904344	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs6934770	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6939873	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7743702	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7755203	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7759420	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7764014	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9320657	0.80[AFR][1000 genomes]
rs9387573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9387582	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9398488	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9401069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9481786	0.82[EUR][1000 genomes]
rs9481788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9481793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9481796	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9481809	0.87[EUR][1000 genomes]
rs9481810	1.00[YRI][hapmap]
rs9481812	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9481818	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9481822	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9481823	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9481824	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9481829	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9481830	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9481835	0.80[AFR][1000 genomes]
rs9489363	1.00[EUR][1000 genomes]
rs9489364	0.82[EUR][1000 genomes]
rs9489365	0.88[AFR][1000 genomes]
rs9489370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489382	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9489398	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9489402	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9489408	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9489410	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9489415	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9489422	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9489430	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9489434	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9489435	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9489451	1.00[ASW][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9489464	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9489468	1.00[ASW][hapmap];0.85[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9489472	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830787	chr6:118631902-118805106	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1025456	chr6:118669672-119058789	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv432958	chr6:118692307-119010307	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv604555	chr6:118695049-118856822	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv1034448	chr6:118698169-119016383	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv1025097	chr6:118699752-119058789	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv1020586	chr6:118711098-118900012	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
14	nsv532052	chr6:118711850-119057295	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv432959	chr6:118716318-119010307	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
16	nsv604556	chr6:118722589-119065365	Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv432960	chr6:118723307-118826307	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
18	nsv525179	chr6:118726243-118876092	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
19	nsv1019357	chr6:118731468-118860705	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9489379	KLF4	trans	brain	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118730400-118745000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:118737800-118748000	Weak transcription	Aorta	Aorta

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