Variant report

Variant	rs3736109
Chromosome Location	chr19:42558629-42558630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42550327..42559850-chr19:42577425..42584775,14	MCF-7	breast:
2	chr19:42558574..42560610-chr19:42573257..42575762,2	MCF-7	breast:
3	chr19:42557311..42558831-chr19:42561689..42563677,2	K562	blood:

Variant related genes	Relation type
ENSG00000105732	Chromatin interaction
ENSG00000268525	Chromatin interaction
ENSG00000105737	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10407506	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10500285	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11878917	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12232804	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16975663	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs16975684	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs17270057	0.89[AMR][1000 genomes]
rs17270169	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs17342067	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs17342179	0.89[AMR][1000 genomes]
rs17342284	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2217342	1.00[YRI][hapmap]
rs2267630	1.00[YRI][hapmap]
rs3810151	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs3826705	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs407096	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs443239	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs454150	0.91[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4803520	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61195828	1.00[ASN][1000 genomes]
rs7248379	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs7251466	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253767	0.87[AMR][1000 genomes]
rs7253791	0.87[AMR][1000 genomes]
rs7253915	0.87[AMR][1000 genomes]
rs8106871	0.87[AMR][1000 genomes]
rs8182491	0.80[CEU][hapmap]
rs899661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3736109	ZNF219	trans	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42539400-42570200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:42539400-42572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:42540400-42572600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:42546600-42559000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:42549800-42563200	Weak transcription	Fetal Intestine Small	intestine
6	chr19:42550400-42559200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:42552200-42570200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr19:42552600-42570200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:42552800-42570000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr19:42552800-42571000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:42553000-42570200	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr19:42553000-42570200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:42553200-42569600	Strong transcription	Brain Germinal Matrix	brain
14	chr19:42553200-42570200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:42553400-42560600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr19:42553400-42570400	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr19:42553600-42570000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:42553800-42560600	Weak transcription	Colon Smooth Muscle	Colon
19	chr19:42553800-42568800	Weak transcription	Primary T cells from cord blood	blood
20	chr19:42553800-42571600	Weak transcription	Spleen	Spleen
21	chr19:42553800-42573200	Weak transcription	Pancreas	Pancrea
22	chr19:42553800-42573200	Weak transcription	Right Atrium	heart
23	chr19:42554400-42567000	Weak transcription	Brain Substantia Nigra	brain
24	chr19:42554400-42570200	Strong transcription	Fetal Stomach	stomach
25	chr19:42554800-42559600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:42554800-42564200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:42555000-42570200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:42555200-42561200	Strong transcription	Brain Cingulate Gyrus	brain
29	chr19:42555200-42561400	Strong transcription	Aorta	Aorta
30	chr19:42555400-42570200	Strong transcription	Stomach Smooth Muscle	stomach
31	chr19:42555600-42570200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:42555800-42561400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:42555800-42564600	Strong transcription	Brain Anterior Caudate	brain
34	chr19:42556000-42563400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr19:42556600-42559000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:42556800-42560800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr19:42556800-42569200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr19:42556800-42570800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:42557000-42559400	Weak transcription	Fetal Brain Male	brain
40	chr19:42557000-42560600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:42557000-42561400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr19:42557000-42562000	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr19:42557000-42568400	Strong transcription	Fetal Brain Female	brain
44	chr19:42557600-42559200	Weak transcription	Fetal Kidney	kidney
45	chr19:42557600-42559800	Strong transcription	Brain Angular Gyrus	brain
46	chr19:42557600-42561200	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr19:42557600-42563200	Weak transcription	Fetal Muscle Leg	muscle
48	chr19:42557800-42563600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr19:42557800-42579200	Weak transcription	Gastric	stomach
50	chr19:42558000-42571600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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