Variant report

Variant	rs4806273
Chromosome Location	chr19:36597239-36597240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:36596983-36603152	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:36596934-36599190	K562	blood:	n/a	n/a
3	BCL3	chr19:36597231-36599406	A549	lung:	n/a	chr19:36599318-36599326
4	POLR2A	chr19:36596949-36597277	K562	blood:	n/a	n/a
5	POLR2A	chr19:36596808-36598636	K562	blood:	n/a	n/a
6	TCF12	chr19:36596795-36597243	SK-N-SH	brain:	n/a	chr19:36597059-36597069
7	POLR2A	chr19:36596890-36597676	K562	blood:	n/a	n/a
8	POLR2A	chr19:36596929-36600393	PANC-1	pancreas:	n/a	n/a
9	TCF12	chr19:36596810-36597382	SK-N-SH	brain:	n/a	chr19:36597059-36597069
10	POLR2A	chr19:36597069-36600450	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr19:36596893-36597579	PFSK-1	brain:	n/a	n/a
12	BCL3	chr19:36597216-36598246	A549	lung:	n/a	n/a
13	POLR2A	chr19:36593610-36600036	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr19:36597074-36598094	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36592203..36593879-chr19:36596112..36598331,2	K562	blood:
2	chr19:36596596..36601731-chr19:36602791..36606754,6	K562	blood:
3	chr19:36588129..36590741-chr19:36597182..36600281,3	MCF-7	breast:
4	chr19:36593550..36596505-chr19:36596648..36599628,2	MCF-7	breast:
5	chr19:36594737..36597838-chr19:36604030..36607473,3	K562	blood:
6	chr19:36543737..36545564-chr19:36596354..36598880,3	MCF-7	breast:

No data

Variant related genes	Relation type
OVOL3	TF binding region
ENSG00000105258	Chromatin interaction
ENSG00000105254	Chromatin interaction
ENSG00000105261	Chromatin interaction
ENSG00000161277	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1009381	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10406862	0.82[ASN][1000 genomes]
rs10418079	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10419924	0.83[ASN][1000 genomes]
rs10420345	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10421377	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10422055	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10425700	0.85[ASN][1000 genomes]
rs10427033	0.85[ASN][1000 genomes]
rs10853945	0.84[EUR][1000 genomes]
rs11538454	0.85[ASN][1000 genomes]
rs11666192	0.89[ASN][1000 genomes]
rs11669890	0.84[ASN][1000 genomes]
rs11879369	0.85[EUR][1000 genomes]
rs12608517	0.85[ASN][1000 genomes]
rs12971639	0.88[EUR][1000 genomes]
rs12971936	0.90[EUR][1000 genomes]
rs12972828	0.88[EUR][1000 genomes]
rs12981698	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12982375	0.84[EUR][1000 genomes]
rs1548506	0.84[EUR][1000 genomes]
rs2023866	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2051800	0.84[EUR][1000 genomes]
rs2074435	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075472	0.89[ASN][1000 genomes]
rs2227260	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2231568	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2301734	0.87[ASN][1000 genomes]
rs2301737	0.89[ASN][1000 genomes]
rs2871649	0.85[ASN][1000 genomes]
rs3810447	0.89[EUR][1000 genomes]
rs4555271	0.83[ASN][1000 genomes]
rs4806262	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4806269	0.82[EUR][1000 genomes]
rs4806271	0.84[ASN][1000 genomes]
rs4806276	0.89[ASN][1000 genomes]
rs55849299	0.83[ASN][1000 genomes]
rs7250364	0.89[ASN][1000 genomes]
rs7251912	0.82[ASN][1000 genomes]
rs7257026	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7258807	0.83[ASN][1000 genomes]
rs73036134	0.88[ASN][1000 genomes]
rs757223	0.84[EUR][1000 genomes]
rs8104047	0.91[EUR][1000 genomes]
rs8104053	0.85[EUR][1000 genomes]
rs8112640	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4806273	POLR2I///RPSA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
2	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
5	chr19:36561200-36597600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr19:36561200-36597600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:36561200-36597600	Strong transcription	Dnd41	blood
8	chr19:36561200-36598200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:36561200-36598400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:36568600-36598000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:36568800-36601400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr19:36570000-36598000	Strong transcription	Fetal Thymus	thymus
13	chr19:36571800-36598400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:36571800-36600000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr19:36571800-36600600	Strong transcription	Fetal Stomach	stomach
16	chr19:36572000-36598000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:36572400-36602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:36573800-36602400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:36574200-36602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:36574600-36604400	Weak transcription	NHDF-Ad	bronchial
21	chr19:36575400-36604200	Weak transcription	Primary B cells from cord blood	blood
22	chr19:36583400-36598000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:36585000-36598200	Strong transcription	Thymus	Thymus
24	chr19:36585000-36601600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr19:36585000-36602400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:36585200-36604400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr19:36587400-36598600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:36587600-36598800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:36588200-36598600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:36588400-36598600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:36588400-36604800	Weak transcription	NH-A	brain
32	chr19:36590200-36598200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:36590200-36600200	Strong transcription	Fetal Brain Female	brain
34	chr19:36590200-36604600	Strong transcription	Fetal Intestine Small	intestine
35	chr19:36590400-36605000	Weak transcription	Aorta	Aorta
36	chr19:36590600-36599400	Strong transcription	Brain Germinal Matrix	brain
37	chr19:36590600-36604800	Weak transcription	Psoas Muscle	Psoas
38	chr19:36591800-36597400	Weak transcription	Brain Anterior Caudate	brain
39	chr19:36591800-36598800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:36592200-36602400	Weak transcription	Brain Substantia Nigra	brain
41	chr19:36592400-36604800	Weak transcription	Right Atrium	heart
42	chr19:36593200-36602600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:36593400-36603400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:36593600-36597600	Strong transcription	Duodenum Mucosa	Duodenum
45	chr19:36594000-36602400	Weak transcription	Fetal Lung	lung
46	chr19:36594000-36603400	Weak transcription	Hela-S3	cervix
47	chr19:36594200-36602400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:36594400-36601400	Weak transcription	Liver	Liver
49	chr19:36594600-36599000	Weak transcription	Ovary	ovary
50	chr19:36594800-36597600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links