Variant report

Variant	rs12684042
Chromosome Location	chr9:16017350-16017351
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10962193	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs10962194	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs11999303	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs12000772	0.88[CHB][hapmap]
rs12005062	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs12682932	0.88[CHB][hapmap];0.88[YRI][hapmap]
rs12683980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12684785	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12684808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12684919	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12686591	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1328266	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1328267	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1328268	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1536685	0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs1578558	0.86[CHB][hapmap]
rs16933805	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16933814	0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs16933967	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16933968	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16933971	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16933973	0.89[ASN][1000 genomes]
rs16933974	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2026660	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2066291	0.88[CHB][hapmap];0.89[YRI][hapmap]
rs2382550	0.86[AFR][1000 genomes]
rs2987082	0.95[AFR][1000 genomes]
rs2987097	0.89[AFR][1000 genomes]
rs3008718	0.92[AFR][1000 genomes]
rs3008720	0.91[AFR][1000 genomes]
rs3008721	0.89[AFR][1000 genomes]
rs3008722	0.94[AFR][1000 genomes]
rs3008724	0.88[AFR][1000 genomes]
rs3008725	0.94[AFR][1000 genomes]
rs3124457	0.92[AFR][1000 genomes]
rs59923163	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60354508	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6475000	0.92[AFR][1000 genomes]
rs7026090	0.88[CHB][hapmap]
rs7029375	0.88[CHB][hapmap]
rs7029410	0.88[CHB][hapmap]
rs7038450	0.81[AFR][1000 genomes]
rs7039881	0.88[CHB][hapmap]
rs7040071	0.86[CHB][hapmap]
rs7040580	0.88[CHB][hapmap]
rs7040928	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7044984	0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs73411567	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73411570	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73411572	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7388793	0.88[CHB][hapmap]
rs770194	0.86[CHB][hapmap]
rs770198	0.88[CHB][hapmap]
rs770199	0.88[CHB][hapmap]
rs770200	0.88[CHB][hapmap]
rs770201	0.88[CHB][hapmap]
rs770202	0.88[CHB][hapmap]
rs7852250	0.88[CHB][hapmap]
rs7866472	0.89[JPT][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs7866699	0.88[CHB][hapmap];0.89[JPT][hapmap];0.89[YRI][hapmap]
rs7867018	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892637	chr9:15926508-16060746	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831521	chr9:15974174-16106565	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16013400-16017600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:16013400-16017800	Weak transcription	Osteobl	bone
3	chr9:16017000-16017800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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