Variant report

Variant	rs7164107
Chromosome Location	chr15:54452793-54452794
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11071049	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12915784	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16974124	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs16974125	0.85[ASN][1000 genomes]
rs16974155	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16974182	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16974217	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1814348	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1864417	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864420	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1897055	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1897058	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1897059	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1897061	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1897064	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2115832	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2115833	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2163200	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2414265	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2414266	0.82[EUR][1000 genomes]
rs28547261	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899524	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4550400	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4550401	0.82[EUR][1000 genomes]
rs4774681	0.81[AFR][1000 genomes]
rs57018516	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs58017453	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59028070	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62009989	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62009990	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166833	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7170148	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7170578	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7174427	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7181337	0.88[ASN][1000 genomes]
rs748288	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7497273	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8032249	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs8039423	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv904226	chr15:53883244-54458310	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv457144	chr15:53890362-54455757	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv569440	chr15:53890362-54455757	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv569441	chr15:53890362-54456754	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv457145	chr15:53890393-54456754	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv569442	chr15:53890393-54456754	Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv428637	chr15:54279125-54500755	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv1048374	chr15:54354984-54484623	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv1043666	chr15:54415970-54548495	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1041282	chr15:54436686-54476135	Flanking Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1037176	chr15:54448271-54471548	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7164107	SCG3	cis	cerebellum	SCAN
rs7164107	NEDD4	cis	parietal	SCAN
rs7164107	SLC24A5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54441800-54453200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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