Variant report

Variant	rs12925296
Chromosome Location	chr16:47069144-47069145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:47062759..47065067-chr16:47066376..47069831,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPT2-2	chr16:47068905-47069296	ENSG00000259821.1

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10459877	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11247542	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11247543	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11859515	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12445492	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12447719	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12596824	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12719759	0.83[EUR][1000 genomes]
rs1362406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1376734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1551188	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894886	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1978336	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2341648	0.94[EUR][1000 genomes]
rs35405784	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4246393	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4577108	1.00[EUR][1000 genomes]
rs4625742	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966781	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4966794	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966795	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4966800	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4967664	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4967696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4967724	0.81[EUR][1000 genomes]
rs4967726	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4967739	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62059134	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7189628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7199379	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7199772	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202325	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7203206	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8046142	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8047353	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052160	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8054039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs8058144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8058714	0.85[EUR][1000 genomes]
rs8060193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9745921	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9923192	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925290	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9925525	0.87[EUR][1000 genomes]
rs9927843	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9939872	1.00[CEU][hapmap];1.00[CHB][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	nsv1059456	chr16:46463770-47307580	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv1066115	chr16:46463770-47318415	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv1056328	chr16:47011193-47172862	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:47064800-47071200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr16:47067400-47070800	Enhancers	GM12878-XiMat	blood
3	chr16:47068000-47071400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:47068600-47071200	Weak transcription	Ovary	ovary
5	chr16:47069000-47069400	Enhancers	Primary B cells from peripheral blood	blood

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