Variant report

Variant	rs367209
Chromosome Location	chr19:44506249-44506250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:44506194-44507446	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:44506211-44507620	HepG2	liver:	n/a	n/a
3	ZNF263	chr19:44506057-44508044	HEK293-T-REx	kidney:	n/a	n/a
4	SREBP1	chr19:44505885-44508675	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:44493777..44495330-chr19:44504111..44506690,2	K562	blood:
2	chr19:44486769..44491037-chr19:44505585..44508395,4	MCF-7	breast:
3	chr19:44506046..44508713-chr19:44597601..44599146,2	MCF-7	breast:
4	chr19:44505664..44508645-chr19:44527908..44530282,2	MCF-7	breast:
5	chr19:44487658..44489792-chr19:44505545..44508358,4	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF230	TF binding region
ENSG00000267680	Chromatin interaction
ENSG00000267144	Chromatin interaction
ENSG00000204920	Chromatin interaction
ENSG00000267022	Chromatin interaction
ENSG00000159885	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10418363	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083732	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083733	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11881151	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12232810	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996408	0.82[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2191566	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2270196	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356549	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35292176	0.83[EUR][1000 genomes]
rs367499	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369106	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377503	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3810406	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs384544	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803667	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803669	0.84[ASN][1000 genomes]
rs4803675	0.86[JPT][hapmap]
rs55703004	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56101767	0.93[EUR][1000 genomes]
rs56171514	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56317065	0.82[ASN][1000 genomes]
rs59963278	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62115482	0.80[ASN][1000 genomes]
rs62119173	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62119176	0.87[ASN][1000 genomes]
rs6509133	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6509138	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7245749	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7252394	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253205	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254261	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7255145	0.91[ASN][1000 genomes]
rs7255315	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7255512	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7256908	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7258517	0.82[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs73037629	0.80[ASN][1000 genomes]
rs8104605	0.86[JPT][hapmap]
rs8105571	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs367209	ZNF223	cis	Thyroid	GTEx
rs367209	FOXA3	cis	cerebellum	SCAN
rs367209	OPA3	cis	cerebellum	SCAN
rs367209	CCDC114	cis	cerebellum	SCAN
rs367209	OPA3	cis	parietal	SCAN
rs367209	HIF3A	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44497000-44506400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:44497000-44506600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:44501000-44506400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:44501000-44506400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:44501200-44506400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr19:44501200-44506400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:44501200-44506400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:44501200-44506400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:44501600-44506400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr19:44501800-44506400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr19:44501800-44506400	Weak transcription	Colonic Mucosa	Colon
12	chr19:44501800-44506400	Weak transcription	Placenta	Placenta
13	chr19:44502000-44506400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:44502000-44506400	Weak transcription	Fetal Thymus	thymus
15	chr19:44502000-44506400	Weak transcription	Ovary	ovary
16	chr19:44502400-44506400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:44502400-44506400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:44502400-44506400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:44502400-44506400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:44502600-44506400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:44502600-44506400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr19:44502800-44506400	Weak transcription	Fetal Stomach	stomach
23	chr19:44505600-44506400	Weak transcription	Gastric	stomach
24	chr19:44506000-44506400	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr19:44506000-44506600	Enhancers	Spleen	Spleen
26	chr19:44506000-44506800	Flanking Active TSS	Dnd41	blood
27	chr19:44506000-44508400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:44506200-44506400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:44506200-44506400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr19:44506200-44506400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr19:44506200-44506400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr19:44506200-44506400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr19:44506200-44506400	Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr19:44506200-44506400	Enhancers	Primary B cells from peripheral blood	blood
35	chr19:44506200-44506400	Active TSS	Primary hematopoietic stem cells	blood
36	chr19:44506200-44506400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:44506200-44506400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr19:44506200-44506400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr19:44506200-44506400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:44506200-44506400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr19:44506200-44506400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr19:44506200-44506400	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr19:44506200-44506400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:44506200-44506400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:44506200-44506400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:44506200-44506400	Active TSS	Brain Angular Gyrus	brain
47	chr19:44506200-44506400	Active TSS	Brain Germinal Matrix	brain
48	chr19:44506200-44506400	Enhancers	Brain Substantia Nigra	brain
49	chr19:44506200-44506400	Enhancers	Colon Smooth Muscle	Colon
50	chr19:44506200-44506400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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