Variant report

Variant	rs12051425
Chromosome Location	chr16:72021962-72021963
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72017350..72022050-chr16:72041006..72044601,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102967	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1035543	0.92[GIH][hapmap];0.84[YRI][hapmap]
rs11642001	0.94[CEU][hapmap]
rs12051517	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs12598018	0.82[ASN][1000 genomes]
rs12600132	0.82[ASN][1000 genomes]
rs12708923	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs13332180	0.92[GIH][hapmap]
rs2303220	0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.92[YRI][hapmap]
rs4538017	0.92[GIH][hapmap]
rs4788567	0.92[GIH][hapmap]
rs4788587	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs4788592	0.87[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs4788593	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs7187692	0.90[CHB][hapmap]
rs7204798	0.93[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs8063499	0.86[CHB][hapmap]
rs952160	0.82[GIH][hapmap]
rs9922596	0.87[ASN][1000 genomes]
rs9925415	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs9928317	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs9933095	0.88[YRI][hapmap]
rs9937465	0.86[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv906894	chr16:72013539-72046211	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12051425	E2F4	cis	cerebellum	SCAN
rs12051425	MARVELD3	cis	lymphoblastoid	seeQTL
rs12051425	TMEM208	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72016200-72022800	Weak transcription	Right Atrium	heart
2	chr16:72021000-72022400	Enhancers	HepG2	liver
3	chr16:72021600-72022800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr16:72021800-72023000	Enhancers	K562	blood

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