Variant report

Variant	rs12513905
Chromosome Location	chr5:57752563-57752564
allele	C/G
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	chr5:57745705-57757136	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr5:57746016-57757149	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr5:57750892-57756934	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr5:57751391-57752625	SK-N-SH	brain:	n/a	n/a
5	SIN3AK20	chr5:57751735-57752673	MCF-7	breast:	n/a	n/a
6	SIN3AK20	chr5:57749882-57757124	MCF-7	breast:	n/a	n/a
7	POLR2A	chr5:57751357-57756911	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr5:57752315-57752565	MCF10A-Er-Src	breast:	n/a	n/a
9	TCF12	chr5:57751726-57752605	A549	lung:	n/a	n/a
10	BCL3	chr5:57751905-57755240	A549	lung:	n/a	n/a
11	POLR2A	chr5:57749894-57752638	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr5:57747447-57756979	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr5:57746933-57752694	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr5:57744593-57752591	A549	lung:	n/a	n/a
15	POLR2A	chr5:57749768-57756922	HUVEC	blood vessel:	n/a	n/a
16	CHD1	chr5:57751128-57757458	IMR90	lung:	n/a	n/a
17	POLR2A	chr5:57745515-57757046	ECC-1	luminal epithelium:	n/a	n/a
18	GATA3	chr5:57746865-57752572	A549	lung:	n/a	chr5:57747131-57747148
19	POLR2A	chr5:57745756-57752683	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
PLK2	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1035484	0.90[AMR][1000 genomes]
rs1035485	0.90[AMR][1000 genomes]
rs1042994	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11546180	0.82[AMR][1000 genomes]
rs12513877	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12522386	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17710502	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17710615	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17767072	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2201293	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2220785	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2408946	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2408947	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs33921924	0.86[AMR][1000 genomes]
rs34150563	0.90[AMR][1000 genomes]
rs34974449	0.90[AMR][1000 genomes]
rs4700289	0.90[AMR][1000 genomes]
rs56286824	0.90[AMR][1000 genomes]
rs56318521	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59135347	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6450474	0.82[AMR][1000 genomes]
rs6879330	0.90[AMR][1000 genomes]
rs6890785	0.82[AMR][1000 genomes]
rs72758162	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7706545	0.82[AMR][1000 genomes]
rs7708381	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7736949	0.90[AMR][1000 genomes]

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57747000-57752800	Weak transcription	Fetal Intestine Small	intestine
2	chr5:57747800-57753000	Strong transcription	Liver	Liver
3	chr5:57747800-57754200	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:57748400-57753400	Strong transcription	Fetal Intestine Large	intestine
5	chr5:57748600-57755000	Transcr. at gene 5' and 3'	A549	lung
6	chr5:57748800-57754200	Weak transcription	Primary B cells from cord blood	blood
7	chr5:57748800-57754600	Weak transcription	Spleen	Spleen
8	chr5:57749000-57754400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr5:57749200-57753000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:57749200-57753400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
11	chr5:57749200-57754600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
12	chr5:57749200-57754800	Transcr. at gene 5' and 3'	HUVEC	blood vessel
13	chr5:57749200-57755000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:57749200-57755000	Transcr. at gene 5' and 3'	NH-A	brain
15	chr5:57749400-57753200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr5:57749400-57753600	Genic enhancers	Fetal Heart	heart
17	chr5:57749600-57753000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:57749600-57753800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:57749600-57754800	Transcr. at gene 5' and 3'	HSMMtube	muscle
20	chr5:57749600-57755000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:57749800-57754600	Transcr. at gene 5' and 3'	HMEC	breast
22	chr5:57750000-57752600	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:57750000-57753000	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr5:57750000-57753200	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr5:57750000-57753200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
26	chr5:57750000-57754600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:57750000-57754600	Transcr. at gene 5' and 3'	NHEK	skin
28	chr5:57750000-57754800	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
29	chr5:57750000-57754800	Transcr. at gene 5' and 3'	HSMM	muscle
30	chr5:57750000-57754800	Transcr. at gene 5' and 3'	Osteobl	bone
31	chr5:57750000-57756800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr5:57750200-57753000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:57750200-57753400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:57750200-57753400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:57750200-57754600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:57750200-57755000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:57750400-57753200	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
38	chr5:57750400-57753600	Weak transcription	Colonic Mucosa	Colon
39	chr5:57750400-57754000	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
40	chr5:57750400-57754200	Weak transcription	Stomach Mucosa	stomach
41	chr5:57750400-57754600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:57750600-57753200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr5:57750600-57754600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:57750800-57753200	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
45	chr5:57750800-57754400	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
46	chr5:57750800-57754800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
47	chr5:57750800-57756800	Active TSS	Right Atrium	heart
48	chr5:57751000-57753200	Transcr. at gene 5' and 3'	Ovary	ovary
49	chr5:57751000-57753400	Genic enhancers	Placenta Amnion	Placenta Amnion
50	chr5:57751000-57753600	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial

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