Variant report

Variant	rs1056772
Chromosome Location	chr4:95585225-95585226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95582862..95585353-chr4:95588857..95590982,2	K562	blood:
2	chr4:95581174..95583133-chr4:95584760..95587422,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10010013	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10014050	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10025288	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10025410	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10049504	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1043862	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097431	0.83[CHD][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs11097432	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1134984	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11550270	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11735212	1.00[CHB][hapmap]
rs12294	0.84[EUR][1000 genomes]
rs12331809	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12331835	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12331920	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1509617	0.83[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17021981	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17336353	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs1802345	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452593	0.81[TSI][hapmap]
rs2452594	0.85[CHB][hapmap]
rs28376560	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28376694	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28654759	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28709926	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3828518	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs6816687	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs6840428	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7655928	1.00[CHB][hapmap];0.84[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7656545	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7679284	0.85[CHB][hapmap]

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	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1056772	PDLIM5	cis	brain	BrainEAC
rs1056772	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95525000-95586400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:95525000-95590000	Weak transcription	Lung	lung
3	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
4	chr4:95533800-95594200	Weak transcription	Gastric	stomach
5	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
6	chr4:95538200-95586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:95538600-95587000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr4:95540000-95587000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
11	chr4:95543000-95586000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:95543000-95586400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:95549000-95586600	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:95557200-95588600	Weak transcription	GM12878-XiMat	blood
15	chr4:95557800-95586200	Weak transcription	Thymus	Thymus
16	chr4:95559000-95590200	Weak transcription	Right Ventricle	heart
17	chr4:95563600-95589000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:95564000-95587000	Weak transcription	NHLF	lung
19	chr4:95564000-95595000	Weak transcription	NHDF-Ad	bronchial
20	chr4:95567800-95587400	Weak transcription	HepG2	liver
21	chr4:95570800-95599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:95571400-95587400	Weak transcription	Fetal Kidney	kidney
23	chr4:95572200-95586400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:95572400-95588800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:95573600-95595000	Weak transcription	Small Intestine	intestine
26	chr4:95574600-95586200	Weak transcription	K562	blood
27	chr4:95574600-95587000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr4:95574800-95591600	Weak transcription	Stomach Mucosa	stomach
29	chr4:95575000-95590800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:95575800-95590200	Strong transcription	Osteobl	bone
31	chr4:95576200-95598000	Weak transcription	Aorta	Aorta
32	chr4:95576200-95598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:95576600-95586800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:95577000-95586800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:95578000-95586800	Strong transcription	HUVEC	blood vessel
36	chr4:95578200-95588200	Strong transcription	Placenta	Placenta
37	chr4:95578400-95586000	Strong transcription	Fetal Intestine Large	intestine
38	chr4:95578400-95586600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:95578600-95589200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:95578600-95593800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:95579000-95592400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:95579600-95586200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr4:95580000-95597800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:95580200-95586800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:95581400-95590000	Strong transcription	NH-A	brain
46	chr4:95581600-95586000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr4:95581800-95585800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr4:95582000-95587000	Weak transcription	HSMMtube	muscle
49	chr4:95582000-95595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:95582000-95599800	Weak transcription	NHEK	skin

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