Variant report

Variant	rs12374075
Chromosome Location	chr3:54314698-54314699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11714935	1.00[YRI][hapmap]
rs12374128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3934631	0.90[TSI][hapmap]
rs3934633	0.95[CHB][hapmap]
rs4078006	0.90[TSI][hapmap];0.80[YRI][hapmap]
rs4078007	0.90[TSI][hapmap];0.80[YRI][hapmap]
rs4257582	0.81[ASW][hapmap];1.00[YRI][hapmap]
rs55725671	0.83[ASN][1000 genomes]
rs55751124	0.84[EUR][1000 genomes]
rs55768606	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55826666	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55982339	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56034762	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56212431	0.86[EUR][1000 genomes]
rs56411589	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57211759	0.85[EUR][1000 genomes]
rs57836319	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59804205	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61200778	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6445640	0.85[EUR][1000 genomes]
rs6766834	1.00[YRI][hapmap]
rs6781457	0.80[YRI][hapmap]
rs6790114	0.80[YRI][hapmap]
rs6792199	0.86[CEU][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs6807491	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap]
rs7427601	0.83[EUR][1000 genomes]
rs7428097	0.86[CHB][hapmap]
rs7432978	0.90[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7434141	0.86[CHB][hapmap]
rs7616934	0.81[ASW][hapmap];1.00[YRI][hapmap]
rs9825336	1.00[YRI][hapmap]
rs9840013	1.00[YRI][hapmap]
rs9844503	0.90[CEU][hapmap]
rs9852538	0.81[ASW][hapmap];0.91[YRI][hapmap]
rs9883365	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1014157	chr3:54168755-54332321	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876806	chr3:54256648-54330010	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12374075	BAP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54313800-54314800	Weak transcription	Esophagus	oesophagus
2	chr3:54313800-54314800	Weak transcription	Right Atrium	heart
3	chr3:54314000-54317000	Weak transcription	Hela-S3	cervix

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