Variant report

Variant	rs11719646
Chromosome Location	chr3:56467691-56467692
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10510786	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11708250	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11712094	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714171	0.84[CEU][hapmap]
rs11715404	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11923602	0.98[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1352765	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1388254	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17056833	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17825463	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55783589	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55801834	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55833786	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56962423	0.81[EUR][1000 genomes]
rs57164168	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57352922	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6801539	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72875310	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72875345	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625995	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs923653	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3383044	chr3:56466497-56483664	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11719646	CCDC66	cis	cerebellum	SCAN
rs11719646	SBNO1	trans	cerebellum	SCAN
rs11719646	RFT1	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56447400-56469200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:56450000-56467800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:56450000-56469800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:56456400-56479600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:56456800-56468000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:56456800-56468400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:56457600-56473400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:56458000-56474800	Weak transcription	Fetal Heart	heart
9	chr3:56458600-56468400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:56465000-56468800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:56465600-56468000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:56465600-56468400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:56466200-56468200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:56466400-56469000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:56466400-56471600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:56466600-56468800	Strong transcription	Brain Germinal Matrix	brain
17	chr3:56467000-56469000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:56467200-56473000	Weak transcription	HUVEC	blood vessel
19	chr3:56467400-56469000	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:56467400-56469000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:56467400-56469000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:56467400-56469000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:56467400-56469000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:56467400-56469000	Strong transcription	Fetal Brain Female	brain
25	chr3:56467600-56468800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:56467600-56469200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:56467600-56469600	Weak transcription	Pancreas	Pancrea
28	chr3:56467600-56470400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:56467600-56470600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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