Variant report

Variant	rs2452600
Chromosome Location	chr4:95496882-95496883
allele	C/T
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	chr4:95496879-95497065	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95496466..95498455-chr4:95499358..95501705,2	K562	blood:

Variant related genes	Relation type
PDLIM5	TF binding region
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12500116	0.81[CEU][hapmap]
rs12510147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13121500	0.85[CEU][hapmap]
rs1493112	0.90[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs1509620	0.83[MEX][hapmap]
rs17021918	0.81[CEU][hapmap]
rs2280003	0.81[CEU][hapmap]
rs2452009	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2452578	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2452597	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452598	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452599	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510767	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs2510770	0.87[EUR][1000 genomes]
rs2510773	0.91[EUR][1000 genomes]
rs2510778	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2577056	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3133150	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35044129	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699316	0.81[CEU][hapmap]
rs4699540	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66542996	0.97[EUR][1000 genomes]
rs6822544	0.80[CEU][hapmap]
rs6845201	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674144	0.81[CEU][hapmap]
rs7681843	0.84[CEU][hapmap]
rs7682375	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2452600	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95483400-95524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:95483800-95497000	Weak transcription	HMEC	breast
3	chr4:95484000-95507400	Weak transcription	Hela-S3	cervix
4	chr4:95489000-95507400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr4:95489200-95506800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr4:95489200-95507400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:95489200-95509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:95489400-95506200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:95489600-95508200	Weak transcription	GM12878-XiMat	blood
10	chr4:95489600-95522800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr4:95489600-95539200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:95492000-95502200	Weak transcription	Fetal Intestine Small	intestine
13	chr4:95492200-95497000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:95493000-95498400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:95493200-95540200	Weak transcription	Small Intestine	intestine
16	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
17	chr4:95493400-95497000	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:95494000-95497800	Genic enhancers	Osteobl	bone
19	chr4:95494000-95506200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:95494400-95497400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:95494600-95497400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:95495200-95506800	Weak transcription	Fetal Stomach	stomach
23	chr4:95495400-95497600	Strong transcription	Placenta	Placenta
24	chr4:95495800-95498200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:95496000-95501800	Weak transcription	Fetal Lung	lung
26	chr4:95496200-95497000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:95496200-95497200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr4:95496200-95498600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
29	chr4:95496400-95497200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr4:95496400-95497400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr4:95496400-95497400	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr4:95496400-95497600	Genic enhancers	Fetal Heart	heart
33	chr4:95496400-95498000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:95496600-95497200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:95496600-95497200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr4:95496600-95497200	Strong transcription	Primary T cells from cord blood	blood
37	chr4:95496600-95497200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:95496600-95497200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr4:95496600-95497200	Genic enhancers	Ovary	ovary
40	chr4:95496600-95497200	Genic enhancers	Rectal Smooth Muscle	rectum
41	chr4:95496600-95497200	Genic enhancers	Right Ventricle	heart
42	chr4:95496600-95497400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:95496600-95497400	Genic enhancers	NHLF	lung
44	chr4:95496600-95497600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:95496600-95497600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr4:95496600-95497600	Strong transcription	Liver	Liver
47	chr4:95496600-95497600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr4:95496600-95497600	Genic enhancers	A549	lung
49	chr4:95496600-95497600	Strong transcription	HepG2	liver
50	chr4:95496600-95497800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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