Variant report

Variant	rs12440270
Chromosome Location	chr15:53804400-53804401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:53058029..53058639-chr15:53804127..53804960,2	MCF-7	breast:
2	chr15:53676316..53677210-chr15:53803959..53804881,5	MCF-7	breast:
3	chr15:53676343..53677288-chr15:53803650..53804851,6	MCF-7	breast:
4	chr15:53057791..53058697-chr15:53803561..53804782,4	MCF-7	breast:
5	chr15:53072513..53073379-chr15:53804086..53804809,3	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10444799	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10444830	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10518727	0.82[ASN][1000 genomes]
rs11070988	0.82[ASN][1000 genomes]
rs11070989	0.82[ASN][1000 genomes]
rs11070990	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1189331	0.82[EUR][1000 genomes]
rs12148070	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12438390	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12440842	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12442849	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12442851	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16966177	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16966184	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16966209	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16966210	0.83[EUR][1000 genomes]
rs17548678	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17630504	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17630697	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1906424	0.82[ASN][1000 genomes]
rs1906425	0.82[ASN][1000 genomes]
rs1906426	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2129774	0.82[ASN][1000 genomes]
rs2220382	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2220383	0.82[ASN][1000 genomes]
rs2414242	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3088091	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3206108	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4531685	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56916135	0.82[ASN][1000 genomes]
rs57855113	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs609401	0.93[ASN][1000 genomes]
rs62005869	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62005872	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62005873	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62005874	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62005881	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62005902	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62005903	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62005905	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62005906	0.82[ASN][1000 genomes]
rs62005908	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62005909	0.82[ASN][1000 genomes]
rs62005911	0.82[ASN][1000 genomes]
rs62005912	0.82[ASN][1000 genomes]
rs62007573	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493631	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7161989	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7162024	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7174349	0.81[EUR][1000 genomes]
rs7174416	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7178004	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73406225	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs74017408	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs74017420	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8030213	0.93[ASN][1000 genomes]
rs8031764	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8041720	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs953521	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	nsv904223	chr15:53665247-54340070	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv904224	chr15:53668018-54210677	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1040216	chr15:53743780-53851679	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv833009	chr15:53752901-53935303	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv569432	chr15:53785483-53811621	Enhancers Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1038512	chr15:53803770-53851679	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12440270	COPS2	cis	cerebellum	SCAN
rs12440270	APOL1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53792200-53806800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:53802000-53804400	Enhancers	HepG2	liver
3	chr15:53802000-53828000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:53802800-53805000	Weak transcription	Liver	Liver
5	chr15:53804200-53821600	Weak transcription	A549	lung

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