Variant report

Variant	rs488416
Chromosome Location	chr3:120630345-120630346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GTF2E1-2	chr3:120630077-120632110	ncRnaDb_ncrna_FR029612_1

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1523507	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1623244	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1683975	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1688683	0.96[EUR][1000 genomes]
rs1688684	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1795414	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2331521	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2331527	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2686651	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108752	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35345840	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3845849	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4510329	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4630876	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs470502	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs470738	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs571545	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589682	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs590436	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590663	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603635	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs603847	0.90[EUR][1000 genomes]
rs619802	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs623175	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs638343	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs661160	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs662110	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs663363	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs680233	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6805670	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6807604	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs682394	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702008	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615991	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7616466	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9844667	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9866746	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9872110	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9883257	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv829700	chr3:120469191-120675763	Strong transcription Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs488416	STXBP5L	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120626400-120630400	Active TSS	Brain Angular Gyrus	brain
2	chr3:120626400-120630400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:120628800-120643800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:120628800-120644000	Weak transcription	Ovary	ovary
5	chr3:120629200-120638000	Weak transcription	Brain Germinal Matrix	brain
6	chr3:120629400-120639200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:120629800-120630800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:120630000-120630400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
9	chr3:120630200-120630800	Enhancers	Pancreatic Islets	Pancreatic Islet

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