Variant report

Variant	rs4699316
Chromosome Location	chr4:95579366-95579367
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10015716	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1043848	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10590	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12500116	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12505788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12510147	0.82[CEU][hapmap]
rs12511169	0.87[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13121500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17021918	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17021972	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2136486	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs2280003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452597	0.81[CEU][hapmap]
rs2452600	0.81[CEU][hapmap]
rs2510767	0.83[CEU][hapmap]
rs35964087	0.91[EUR][1000 genomes]
rs3762876	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61597100	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6817664	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6822544	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6837308	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7659399	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7674144	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7681843	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7694162	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998071	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4699316	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
2	chr4:95525000-95586400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:95525000-95590000	Weak transcription	Lung	lung
4	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
5	chr4:95533800-95594200	Weak transcription	Gastric	stomach
6	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
7	chr4:95538000-95585200	Weak transcription	Colonic Mucosa	Colon
8	chr4:95538200-95582600	Weak transcription	Hela-S3	cervix
9	chr4:95538200-95586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:95538600-95587000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr4:95540000-95587000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
14	chr4:95541400-95580200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:95543000-95586000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:95543000-95586400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:95549000-95586600	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:95555200-95581800	Weak transcription	Ovary	ovary
19	chr4:95557200-95588600	Weak transcription	GM12878-XiMat	blood
20	chr4:95557400-95583800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:95557800-95586200	Weak transcription	Thymus	Thymus
22	chr4:95558200-95580800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr4:95559000-95590200	Weak transcription	Right Ventricle	heart
24	chr4:95561400-95585200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr4:95561600-95580200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:95563200-95584400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:95563600-95583400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr4:95563600-95589000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr4:95563800-95579400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:95563800-95583400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:95563800-95583400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:95564000-95581200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:95564000-95587000	Weak transcription	NHLF	lung
34	chr4:95564000-95595000	Weak transcription	NHDF-Ad	bronchial
35	chr4:95567800-95582200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:95567800-95587400	Weak transcription	HepG2	liver
37	chr4:95570000-95581800	Weak transcription	Esophagus	oesophagus
38	chr4:95570400-95581000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:95570800-95582800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:95570800-95599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:95571400-95587400	Weak transcription	Fetal Kidney	kidney
42	chr4:95571600-95581400	Weak transcription	Fetal Muscle Leg	muscle
43	chr4:95571800-95580600	Strong transcription	HSMM	muscle
44	chr4:95572200-95583200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:95572200-95586400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:95572400-95588800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr4:95573600-95595000	Weak transcription	Small Intestine	intestine
48	chr4:95574600-95586200	Weak transcription	K562	blood
49	chr4:95574600-95587000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr4:95574800-95591600	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links