Variant report

Variant	rs470647
Chromosome Location	chr3:120628840-120628841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11918518	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4306806	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs470699	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55989794	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs588620	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591475	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs612545	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs638724	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9833801	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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	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
6	esv3431805	chr3:120626112-120628860	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs470647	PARP9	cis	cerebellum	SCAN
rs470647	STXBP5L	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120626200-120629000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:120626200-120630200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:120626400-120629200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:120626400-120630400	Active TSS	Brain Angular Gyrus	brain
5	chr3:120626400-120630400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr3:120626600-120629400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:120627000-120629000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:120627800-120629000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr3:120628000-120629000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr3:120628000-120629200	Active TSS	Brain Germinal Matrix	brain
11	chr3:120628200-120629200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
12	chr3:120628400-120629000	Bivalent Enhancer	Primary B cells from cord blood	blood
13	chr3:120628400-120629400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:120628600-120629000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
15	chr3:120628600-120629000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:120628600-120629000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:120628600-120629000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:120628600-120629400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
19	chr3:120628800-120629000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr3:120628800-120629000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
21	chr3:120628800-120629000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr3:120628800-120629000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:120628800-120629200	Active TSS	Brain Cingulate Gyrus	brain
24	chr3:120628800-120629800	Weak transcription	Fetal Brain Male	brain
25	chr3:120628800-120643800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:120628800-120644000	Weak transcription	Ovary	ovary

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