Variant report

Variant	rs12439644
Chromosome Location	chr15:53682368-53682369
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10083669	0.93[EUR][1000 genomes]
rs1038552	0.82[EUR][1000 genomes]
rs1038553	0.96[EUR][1000 genomes]
rs11630701	0.93[EUR][1000 genomes]
rs11635444	0.93[EUR][1000 genomes]
rs11635520	0.93[EUR][1000 genomes]
rs11635540	0.93[EUR][1000 genomes]
rs12148424	0.98[EUR][1000 genomes]
rs12148432	0.98[EUR][1000 genomes]
rs1356242	0.93[EUR][1000 genomes]
rs1356243	0.93[EUR][1000 genomes]
rs1400212	0.96[EUR][1000 genomes]
rs1400213	0.96[EUR][1000 genomes]
rs1400214	0.98[EUR][1000 genomes]
rs1400215	0.96[EUR][1000 genomes]
rs1501067	0.95[EUR][1000 genomes]
rs1501068	0.95[EUR][1000 genomes]
rs1516407	0.97[EUR][1000 genomes]
rs1516408	0.95[EUR][1000 genomes]
rs1516409	0.95[EUR][1000 genomes]
rs1516410	0.96[EUR][1000 genomes]
rs1516414	0.95[EUR][1000 genomes]
rs2055404	0.93[EUR][1000 genomes]
rs2055405	0.93[EUR][1000 genomes]
rs2055406	0.96[EUR][1000 genomes]
rs2414233	0.95[EUR][1000 genomes]
rs4776139	0.93[EUR][1000 genomes]
rs4776140	0.99[EUR][1000 genomes]
rs592248	0.95[EUR][1000 genomes]
rs6493622	0.95[EUR][1000 genomes]
rs7168732	0.98[EUR][1000 genomes]
rs7169090	0.99[EUR][1000 genomes]
rs7169159	0.96[EUR][1000 genomes]
rs7169275	0.99[EUR][1000 genomes]
rs8036605	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8037058	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8037474	0.98[EUR][1000 genomes]
rs972893	0.93[EUR][1000 genomes]
rs974730	0.95[EUR][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	nsv1037630	chr15:53324645-53708925	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv833008	chr15:53630471-53780618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	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
4	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
5	nsv1049319	chr15:53671945-53785267	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1050374	chr15:53674726-53785267	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12439644	SPPL2A	cis	cerebellum	SCAN
rs12439644	SERTAD4	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:53681600-53682400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:53681800-53682400	Enhancers	H1 Cell Line	embryonic stem cell
3	chr15:53682000-53682400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr15:53682000-53682600	Enhancers	HUES64 Cell Line	embryonic stem cell

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