Variant report

Variant	rs1852148
Chromosome Location	chr12:85435434-85435435
allele	C/T
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	GATA3	chr12:85435162-85435680	T-47D	breast:	n/a	n/a
2	EP300	chr12:85435147-85435689	T-47D	breast:	n/a	n/a
3	FOXA1	chr12:85435173-85435705	T-47D	breast:	n/a	n/a
4	FOXA1	chr12:85435157-85435961	T-47D	breast:	n/a	chr12:85435828-85435840
5	GATA3	chr12:85435138-85435651	T-47D	breast:	n/a	n/a
6	JUND	chr12:85435242-85435877	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
LRRIQ1	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1031190	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12227853	1.00[CEU][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs12301980	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12304556	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1494500	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1494501	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1525548	0.89[EUR][1000 genomes]
rs168613	0.95[CEU][hapmap]
rs168615	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1690835	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1973816	0.89[EUR][1000 genomes]
rs2056638	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2660449	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2660454	0.84[AMR][1000 genomes]
rs2660455	0.84[AMR][1000 genomes]
rs2660459	0.83[AMR][1000 genomes]
rs2708496	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2708498	0.82[AMR][1000 genomes]
rs359992	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs6539879	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6539881	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7132596	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7133817	1.00[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7302312	0.84[AMR][1000 genomes]
rs7316900	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7954110	0.89[EUR][1000 genomes]
rs7962411	0.89[EUR][1000 genomes]
rs7962577	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs796567	0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs7974418	1.00[CEU][hapmap];0.96[MEX][hapmap]

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	nsv899377	chr12:85157346-85629241	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1040452	chr12:85179586-85747907	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1792335	chr12:85321249-86003609	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv899387	chr12:85427691-85629241	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv455669	chr12:85427691-85638089	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv559653	chr12:85427691-85638089	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv899388	chr12:85427691-85766847	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv899389	chr12:85430187-85499132	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1852148	MYF5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85431200-85441200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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