Variant report

Variant	rs9989683
Chromosome Location	chr19:36547530-36547531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36547510-36547728	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36497884..36507784-chr19:36542079..36547610,17	MCF-7	breast:
2	chr19:36484913..36488286-chr19:36544915..36548972,3	MCF-7	breast:
3	chr19:36484438..36486588-chr19:36547484..36549798,2	K562	blood:
4	chr19:36543835..36550918-chr19:36603651..36608049,11	MCF-7	breast:

Variant related genes	Relation type
THAP8	TF binding region
ENSG00000205138	Chromatin interaction
ENSG00000239382	Chromatin interaction
ENSG00000181392	Chromatin interaction
ENSG00000105258	Chromatin interaction
ENSG00000105261	Chromatin interaction
ENSG00000105254	Chromatin interaction
ENSG00000267698	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10410926	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13344701	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13344825	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17777328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2074436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2239509	0.87[JPT][hapmap]
rs2285425	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28514579	0.86[ASN][1000 genomes]
rs34250145	1.00[GIH][hapmap]
rs35759606	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3810449	0.84[CHB][hapmap]
rs3810450	0.84[CHB][hapmap]
rs4806277	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7257598	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7257665	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9989683	PSG1	cis	cerebellum	SCAN
rs9989683	CLIPR-59	cis	multi-tissue	Pritchard
rs9989683	PLEKHG2	cis	cerebellum	SCAN
rs9989683	ZNF573	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36544200-36547600	Active TSS	NHLF	lung
2	chr19:36544600-36547600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr19:36546200-36547800	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr19:36546400-36547800	Enhancers	Stomach Mucosa	stomach
5	chr19:36546400-36549600	Weak transcription	Gastric	stomach
6	chr19:36546400-36577600	Weak transcription	Esophagus	oesophagus
7	chr19:36546400-36584000	Weak transcription	Right Atrium	heart
8	chr19:36546600-36547600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:36546600-36547600	Enhancers	Fetal Lung	lung
10	chr19:36546600-36547600	Transcr. at gene 5' and 3'	A549	lung
11	chr19:36546600-36548000	Enhancers	Fetal Muscle Trunk	muscle
12	chr19:36546600-36549200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr19:36546600-36549400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:36546600-36549400	Weak transcription	Liver	Liver
15	chr19:36546600-36549400	Weak transcription	Psoas Muscle	Psoas
16	chr19:36546600-36549400	Weak transcription	HSMMtube	muscle
17	chr19:36546600-36551000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:36546600-36551200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr19:36546600-36551200	Weak transcription	Brain Substantia Nigra	brain
20	chr19:36546600-36551600	Weak transcription	Brain Angular Gyrus	brain
21	chr19:36546600-36551600	Weak transcription	Brain Anterior Caudate	brain
22	chr19:36546600-36551600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:36546600-36556600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:36546600-36556800	Weak transcription	Spleen	Spleen
25	chr19:36546600-36557800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:36546600-36572400	Weak transcription	Lung	lung
27	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
28	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr19:36546800-36547600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:36546800-36547600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:36546800-36547600	Enhancers	Fetal Heart	heart
32	chr19:36546800-36547600	Enhancers	HUVEC	blood vessel
33	chr19:36546800-36547800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:36546800-36547800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr19:36546800-36548000	Enhancers	Fetal Stomach	stomach
36	chr19:36546800-36549400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr19:36546800-36549400	Weak transcription	Fetal Intestine Large	intestine
38	chr19:36546800-36549400	Weak transcription	Fetal Intestine Small	intestine
39	chr19:36546800-36550000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:36546800-36551600	Weak transcription	Brain Hippocampus Middle	brain
41	chr19:36546800-36551800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:36546800-36551800	Weak transcription	HSMM	muscle
43	chr19:36546800-36557800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:36546800-36572000	Weak transcription	Primary T cells from cord blood	blood
45	chr19:36546800-36572800	Weak transcription	Primary B cells from cord blood	blood
46	chr19:36546800-36572800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr19:36546800-36580200	Weak transcription	Fetal Kidney	kidney
48	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum

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