Variant report

Variant	rs7515001
Chromosome Location	chr1:171356755-171356756
allele	A/G
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	FOS	chr1:171356638-171357001	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:171356698-171356997	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr1:171356706-171356972	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr1:171356706-171356906	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:171356602-171356757	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr1:171356704-171356951	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr1:171356720-171356946	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:171356637-171357001	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
GM2AP2	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10157634	0.80[AMR][1000 genomes]
rs1018392	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10912810	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs10912872	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11807475	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12406999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737633	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap]
rs12739998	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1963273	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes]
rs2011345	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs2011548	0.80[AMR][1000 genomes]
rs2223477	0.90[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap]
rs2235510	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap]
rs4916225	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6662297	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6670432	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs6670627	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs6688317	0.80[AMR][1000 genomes]
rs6699676	0.81[AMR][1000 genomes]
rs7516677	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002423	chr1:171294384-171376936	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv548188	chr1:171308832-171371998	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7515001	FMO2	cis	cerebellum	SCAN
rs7515001	PRDX6	cis	cerebellum	SCAN
rs7515001	FMO4	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171351600-171372600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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