Variant report

Variant	rs2872375
Chromosome Location	chr3:78295664-78295665
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12631515	0.83[ASN][1000 genomes]
rs12631676	0.87[ASN][1000 genomes]
rs12632339	1.00[ASN][1000 genomes]
rs12635998	0.81[ASN][1000 genomes]
rs12636011	0.81[ASN][1000 genomes]
rs12636583	0.81[ASN][1000 genomes]
rs12638712	0.88[ASN][1000 genomes]
rs12639191	0.86[ASN][1000 genomes]
rs12639209	0.86[ASN][1000 genomes]
rs13096355	1.00[ASN][1000 genomes]
rs1398328	0.87[ASN][1000 genomes]
rs1398329	0.87[ASN][1000 genomes]
rs1398330	0.87[ASN][1000 genomes]
rs1398331	0.87[ASN][1000 genomes]
rs17777319	1.00[ASN][1000 genomes]
rs17777549	0.81[ASN][1000 genomes]
rs17833836	0.93[ASN][1000 genomes]
rs17834090	0.83[ASN][1000 genomes]
rs1858425	0.81[ASN][1000 genomes]
rs1917097	1.00[ASN][1000 genomes]
rs1917098	1.00[ASN][1000 genomes]
rs1917099	0.99[ASN][1000 genomes]
rs1917100	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917102	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2140645	0.86[ASN][1000 genomes]
rs35884433	1.00[ASN][1000 genomes]
rs36044834	1.00[ASN][1000 genomes]
rs58383444	0.83[ASN][1000 genomes]
rs58971449	0.83[ASN][1000 genomes]
rs62254596	0.84[ASN][1000 genomes]
rs62254597	0.87[ASN][1000 genomes]
rs62254599	0.87[ASN][1000 genomes]
rs62254600	0.87[ASN][1000 genomes]
rs62254601	0.86[ASN][1000 genomes]
rs62254603	0.86[ASN][1000 genomes]
rs62254606	0.86[ASN][1000 genomes]
rs62254607	0.83[ASN][1000 genomes]
rs62254610	0.83[ASN][1000 genomes]
rs62254611	0.83[ASN][1000 genomes]
rs62254612	0.81[ASN][1000 genomes]
rs62254613	0.81[ASN][1000 genomes]
rs62254614	0.81[ASN][1000 genomes]
rs62256248	0.94[ASN][1000 genomes]
rs62256250	0.93[ASN][1000 genomes]
rs62256251	1.00[ASN][1000 genomes]
rs62256252	0.93[ASN][1000 genomes]
rs62256253	0.93[ASN][1000 genomes]
rs62256254	0.88[ASN][1000 genomes]
rs62256256	0.90[ASN][1000 genomes]
rs62256259	0.87[ASN][1000 genomes]
rs67330234	1.00[ASN][1000 genomes]
rs6766104	0.99[ASN][1000 genomes]
rs6776916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777743	0.87[ASN][1000 genomes]
rs6778976	0.99[ASN][1000 genomes]
rs6782991	0.86[ASN][1000 genomes]
rs6783421	0.86[ASN][1000 genomes]
rs925504	0.87[ASN][1000 genomes]
rs9844417	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877017	chr3:77881397-78670654	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1008290	chr3:77895292-78308583	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv536595	chr3:77895292-78308583	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv529995	chr3:78188643-78739698	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv460726	chr3:78295664-78455767	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv590733	chr3:78295664-78455767	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2872375	GBE1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78295400-78295800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
2	chr3:78295400-78295800	ZNF genes & repeats	Fetal Lung	lung
3	chr3:78295400-78296200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:78295400-78296200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:78295600-78296200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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