Variant report

Variant	rs28582311
Chromosome Location	chr4:95547412-95547413
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10010013	0.87[EUR][1000 genomes]
rs10014050	0.88[EUR][1000 genomes]
rs11097431	0.80[EUR][1000 genomes]
rs17336353	0.82[EUR][1000 genomes]
rs3912820	0.88[ASN][1000 genomes]
rs6816687	0.80[EUR][1000 genomes]
rs7655928	0.86[EUR][1000 genomes]
rs7656545	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28582311	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 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	chr4:95497200-95553000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:95497200-95569400	Weak transcription	Esophagus	oesophagus
4	chr4:95507200-95548200	Weak transcription	Psoas Muscle	Psoas
5	chr4:95507200-95548600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:95511200-95554800	Weak transcription	NHDF-Ad	bronchial
7	chr4:95515000-95562000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:95525000-95569600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:95525000-95586400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:95525000-95590000	Weak transcription	Lung	lung
11	chr4:95525400-95562200	Weak transcription	NHLF	lung
12	chr4:95526800-95551000	Weak transcription	Brain Anterior Caudate	brain
13	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
14	chr4:95528000-95555000	Weak transcription	Aorta	Aorta
15	chr4:95533800-95594200	Weak transcription	Gastric	stomach
16	chr4:95537000-95563000	Weak transcription	K562	blood
17	chr4:95537600-95573400	Weak transcription	Spleen	Spleen
18	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
19	chr4:95538000-95585200	Weak transcription	Colonic Mucosa	Colon
20	chr4:95538200-95555200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:95538200-95582600	Weak transcription	Hela-S3	cervix
22	chr4:95538200-95586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:95538600-95587000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr4:95538800-95547800	Weak transcription	Brain Angular Gyrus	brain
25	chr4:95539000-95553600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:95539800-95561000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:95540000-95560600	Weak transcription	HepG2	liver
28	chr4:95540000-95566800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:95540000-95587000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:95540400-95558600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:95540400-95561400	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:95540400-95570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:95540600-95555000	Weak transcription	Ovary	ovary
35	chr4:95541000-95572600	Weak transcription	Small Intestine	intestine
36	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
37	chr4:95541400-95550800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:95541400-95554800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:95541400-95558800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr4:95541400-95559200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr4:95541400-95560800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr4:95541400-95561200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr4:95541400-95580200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr4:95541600-95554800	Weak transcription	Right Ventricle	heart
45	chr4:95541600-95561600	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr4:95541600-95571400	Weak transcription	Fetal Muscle Leg	muscle
47	chr4:95541800-95555000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:95542000-95550200	Weak transcription	Fetal Intestine Small	intestine
49	chr4:95543000-95586000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr4:95543000-95586400	Weak transcription	Primary hematopoietic stem cells	blood

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