Variant report

Variant	rs16839427
Chromosome Location	chr3:97939961-97939962
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	BRCA1	chr3:97939937-97940001	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
OR5H4P	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1008191	0.85[AMR][1000 genomes]
rs10935236	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs11720035	0.84[ASN][1000 genomes]
rs11917362	0.82[AMR][1000 genomes]
rs11929098	0.85[AMR][1000 genomes]
rs12489147	0.81[JPT][hapmap]
rs12632368	0.85[AMR][1000 genomes]
rs12632378	0.87[AMR][1000 genomes]
rs12633948	0.80[AMR][1000 genomes]
rs12636903	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12636942	0.85[AMR][1000 genomes]
rs12637340	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12637769	0.85[AMR][1000 genomes]
rs12638749	0.85[AMR][1000 genomes]
rs12638827	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13066311	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13075581	0.85[AMR][1000 genomes]
rs13079269	0.87[AMR][1000 genomes]
rs13080412	0.85[AMR][1000 genomes]
rs13080694	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13086001	0.85[AMR][1000 genomes]
rs13088051	0.85[AMR][1000 genomes]
rs13090539	0.82[AMR][1000 genomes]
rs13096400	0.85[AMR][1000 genomes]
rs1391152	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1548141	0.89[ASN][1000 genomes]
rs16839430	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16839647	0.85[AMR][1000 genomes]
rs2132890	0.82[AMR][1000 genomes]
rs2132891	0.82[AMR][1000 genomes]
rs2132898	0.85[AMR][1000 genomes]
rs2316269	0.85[AMR][1000 genomes]
rs34127316	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34298341	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34616628	0.84[AMR][1000 genomes]
rs34721537	0.87[AMR][1000 genomes]
rs34745979	0.81[AMR][1000 genomes]
rs34795831	0.89[ASN][1000 genomes]
rs34829706	0.87[AMR][1000 genomes]
rs35015849	0.82[AMR][1000 genomes]
rs35133117	0.87[AMR][1000 genomes]
rs35212708	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35370148	0.87[AMR][1000 genomes]
rs35468350	0.84[AMR][1000 genomes]
rs35584221	0.85[AMR][1000 genomes]
rs35866150	0.84[AMR][1000 genomes]
rs36064521	0.85[AMR][1000 genomes]
rs3736345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4241472	1.00[GIH][hapmap];0.86[TSI][hapmap]
rs4519740	0.85[AMR][1000 genomes]
rs4574333	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4857086	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4857363	0.82[AMR][1000 genomes]
rs56220142	0.87[AMR][1000 genomes]
rs58407128	0.84[AMR][1000 genomes]
rs59697145	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6439696	0.89[ASN][1000 genomes]
rs66498739	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783261	0.81[JPT][hapmap]
rs6805802	0.85[AMR][1000 genomes]
rs71311371	0.87[AMR][1000 genomes]
rs72931007	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641621	0.85[AMR][1000 genomes]
rs7641820	0.85[AMR][1000 genomes]
rs9790053	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869347	chr3:97742604-98051633	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv877209	chr3:97806616-98049409	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv963576	chr3:97825434-98041343	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1004820	chr3:97852875-98169488	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv834773	chr3:97855362-98043888	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1000834	chr3:97859880-98095473	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv877210	chr3:97866177-97992964	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv870074	chr3:97903273-97948850	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv2763288	chr3:97908670-97947253	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription	TF binding region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv432462	chr3:97918267-98001710	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv877211	chr3:97919363-97958280	Active TSS Weak transcription Enhancers Flanking Active TSS	TF binding region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv591063	chr3:97924688-97958280	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv591064	chr3:97931105-97958280	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv877212	chr3:97931105-98033400	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	esv1842860	chr3:97934241-98075543	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv1004762	chr3:97935701-98000227	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
17	nsv1008569	chr3:97937168-97983117	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:97937800-97942400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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