Variant report

Variant	rs12725915
Chromosome Location	chr1:170263540-170263541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10753803	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10800510	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800511	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11577543	0.96[ASN][1000 genomes]
rs11579802	0.85[ASN][1000 genomes]
rs11582930	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585499	0.85[ASN][1000 genomes]
rs11802454	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11802884	0.94[ASN][1000 genomes]
rs12404913	0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12738543	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12745998	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1332955	0.91[EUR][1000 genomes]
rs2027010	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2095134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2151244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2151245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2184041	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2184042	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251095	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2254605	0.92[EUR][1000 genomes]
rs2254608	0.92[EUR][1000 genomes]
rs2254609	0.92[EUR][1000 genomes]
rs2265323	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2990635	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2990637	0.92[EUR][1000 genomes]
rs2990638	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2990639	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2990641	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2998163	0.92[EUR][1000 genomes]
rs2998165	0.92[EUR][1000 genomes]
rs2998166	0.85[EUR][1000 genomes]
rs34335232	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35038938	0.88[ASN][1000 genomes]
rs35102909	0.90[ASN][1000 genomes]
rs3795614	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3795615	0.92[EUR][1000 genomes]
rs55834059	0.95[ASN][1000 genomes]
rs56185457	0.96[ASN][1000 genomes]
rs61827994	0.86[ASN][1000 genomes]
rs61827996	0.87[ASN][1000 genomes]
rs6700678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72703813	0.81[ASN][1000 genomes]
rs7522187	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7524746	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7538465	0.87[ASN][1000 genomes]

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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12725915	DNM3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170254600-170267800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:170260400-170265200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:170261400-170265800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:170261600-170263800	Weak transcription	NHDF-Ad	bronchial
5	chr1:170263200-170264000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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