Variant report

Variant	rs3745233
Chromosome Location	chr19:42733865-42733866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42733570..42735969-chr19:42900000..42902520,2	K562	blood:
2	chr19:42704957..42708119-chr19:42733053..42736266,3	K562	blood:
3	chr19:42733569..42736510-chr19:42736596..42742649,6	MCF-7	breast:
4	chr19:42732520..42734160-chr19:42754071..42756928,2	MCF-7	breast:
5	chr19:42732938..42734464-chr19:42741874..42743780,2	MCF-7	breast:
6	chr19:42637111..42637810-chr19:42733569..42734439,2	K562	blood:
7	chr19:42733053..42735224-chr19:58905022..58907163,2	K562	blood:

Variant related genes	Relation type
ENSG00000105723	Chromatin interaction
ENSG00000105722	Chromatin interaction
ENSG00000266226	Chromatin interaction
ENSG00000213904	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10407506	0.80[LWK][hapmap]
rs10410185	0.82[CHB][hapmap]
rs10410198	0.82[CHB][hapmap]
rs10410698	0.82[CHB][hapmap]
rs10500285	0.93[GIH][hapmap];0.83[TSI][hapmap]
rs11878620	0.81[ASW][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs11880124	0.81[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11883412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1206009	0.82[CHB][hapmap]
rs1206027	0.82[CHB][hapmap]
rs1206029	0.82[CHB][hapmap]
rs1206033	0.82[CHB][hapmap]
rs1206038	0.82[CHB][hapmap]
rs1206040	0.82[CHB][hapmap]
rs1206041	0.82[CHB][hapmap]
rs1206044	0.82[CHB][hapmap]
rs1613100	0.82[CHB][hapmap]
rs1654623	0.82[CHB][hapmap]
rs1676211	0.82[CHB][hapmap]
rs1676217	0.82[CHB][hapmap]
rs1676221	0.82[CHB][hapmap]
rs1676222	0.82[CHB][hapmap]
rs1685565	0.82[CHB][hapmap]
rs16975663	0.83[ASW][hapmap];0.90[CEU][hapmap];0.83[GIH][hapmap];0.94[LWK][hapmap];0.94[YRI][hapmap]
rs16975684	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17270169	0.85[CHB][hapmap];0.93[GIH][hapmap];0.83[TSI][hapmap]
rs17342284	0.85[CHB][hapmap]
rs2267630	0.82[CHB][hapmap]
rs2302485	0.93[GIH][hapmap];0.91[MEX][hapmap]
rs2303652	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2537697	0.82[CHB][hapmap]
rs2615614	0.82[CHB][hapmap]
rs28621009	0.82[CHB][hapmap]
rs3745231	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810148	0.82[CHB][hapmap]
rs3810151	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3826705	0.93[GIH][hapmap]
rs4141062	0.82[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs59099214	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7248379	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs741070	0.82[CHB][hapmap]
rs8108096	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182491	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs851296	0.82[CHB][hapmap]
rs9636121	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
9	nsv961292	chr19:42710814-42734591	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
10	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3745233	ZNF219	trans	lymphoblastoid	RTeQTL
rs3745233	DEDD2	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42725000-42747000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:42725200-42735000	Weak transcription	Small Intestine	intestine
3	chr19:42725400-42745200	Weak transcription	Fetal Brain Male	brain
4	chr19:42725600-42744000	Weak transcription	Right Atrium	heart
5	chr19:42725600-42745000	Weak transcription	Fetal Heart	heart
6	chr19:42726400-42734200	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr19:42726400-42741600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:42726600-42741400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:42726800-42734200	Strong transcription	Placenta	Placenta
10	chr19:42726800-42741200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr19:42726800-42744000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr19:42726800-42745000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:42727000-42739600	Strong transcription	Thymus	Thymus
14	chr19:42727000-42745000	Weak transcription	Hela-S3	cervix
15	chr19:42727200-42737600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr19:42728000-42737600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:42728200-42734400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:42728200-42737400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:42728200-42737800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr19:42728200-42741400	Strong transcription	Fetal Lung	lung
21	chr19:42728200-42744000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:42728400-42734000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:42728400-42734200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr19:42728400-42736600	Strong transcription	Primary hematopoietic stem cells	blood
25	chr19:42728400-42737400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr19:42728400-42737800	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:42728400-42741000	Strong transcription	HUVEC	blood vessel
28	chr19:42728400-42741200	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr19:42728400-42741200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr19:42728400-42741200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr19:42728400-42741200	Strong transcription	Liver	Liver
32	chr19:42728400-42741200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr19:42728400-42741200	Strong transcription	Fetal Brain Female	brain
34	chr19:42728400-42741200	Strong transcription	Left Ventricle	heart
35	chr19:42728400-42741200	Strong transcription	Lung	lung
36	chr19:42728400-42741200	Strong transcription	Rectal Smooth Muscle	rectum
37	chr19:42728400-42741400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:42728400-42741400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:42728400-42741400	Strong transcription	Brain Germinal Matrix	brain
40	chr19:42728400-42741400	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr19:42728400-42741600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:42728400-42741800	Strong transcription	Primary T cells from cord blood	blood
43	chr19:42728400-42741800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr19:42728400-42742000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr19:42728400-42743200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:42728400-42743600	Strong transcription	Dnd41	blood
47	chr19:42728400-42744800	Strong transcription	Fetal Thymus	thymus
48	chr19:42728600-42734000	Strong transcription	Colon Smooth Muscle	Colon
49	chr19:42728600-42741400	Strong transcription	Primary B cells from cord blood	blood
50	chr19:42728600-42741600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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