Variant report

Variant	rs28654759
Chromosome Location	chr4:95589897-95589898
allele	C/T
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:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10010013	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10014050	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10025288	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025410	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049504	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1043862	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056772	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097431	0.81[EUR][1000 genomes]
rs11097432	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134984	0.92[EUR][1000 genomes]
rs11550270	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12294	0.90[EUR][1000 genomes]
rs12331809	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331835	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331920	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509617	0.92[EUR][1000 genomes]
rs17021981	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17336353	0.81[EUR][1000 genomes]
rs1802345	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376560	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376694	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28479946	0.83[EUR][1000 genomes]
rs28709926	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828518	0.81[EUR][1000 genomes]
rs6816687	0.81[EUR][1000 genomes]
rs6840428	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7285	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655928	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656545	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[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
rs28654759	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95525000-95590000	Weak transcription	Lung	lung
2	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
3	chr4:95533800-95594200	Weak transcription	Gastric	stomach
4	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
5	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
7	chr4:95559000-95590200	Weak transcription	Right Ventricle	heart
8	chr4:95564000-95595000	Weak transcription	NHDF-Ad	bronchial
9	chr4:95570800-95599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:95573600-95595000	Weak transcription	Small Intestine	intestine
11	chr4:95574800-95591600	Weak transcription	Stomach Mucosa	stomach
12	chr4:95575000-95590800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:95575800-95590200	Strong transcription	Osteobl	bone
14	chr4:95576200-95598000	Weak transcription	Aorta	Aorta
15	chr4:95576200-95598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:95578600-95593800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:95579000-95592400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:95580000-95597800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:95581400-95590000	Strong transcription	NH-A	brain
20	chr4:95582000-95595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:95582000-95599800	Weak transcription	NHEK	skin
22	chr4:95582400-95592200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:95582400-95594200	Weak transcription	Esophagus	oesophagus
24	chr4:95582400-95596200	Weak transcription	Fetal Muscle Leg	muscle
25	chr4:95582400-95598200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:95582600-95593800	Weak transcription	Ovary	ovary
27	chr4:95582600-95600000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:95582800-95598000	Weak transcription	Fetal Heart	heart
29	chr4:95585000-95592200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:95585200-95592200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:95585200-95592200	Weak transcription	Adipose Nuclei	Adipose
32	chr4:95585200-95593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:95585200-95598200	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:95585800-95590400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr4:95586000-95594000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr4:95586000-95598000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:95586600-95594000	Weak transcription	Fetal Intestine Small	intestine
38	chr4:95586600-95594200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:95587400-95590200	Strong transcription	HMEC	breast
40	chr4:95587400-95598000	Weak transcription	HSMMtube	muscle
41	chr4:95587600-95590000	Weak transcription	Fetal Kidney	kidney
42	chr4:95587600-95590200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:95587600-95590800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:95587600-95591000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:95587600-95591200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:95587600-95592200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:95587600-95592200	Weak transcription	Left Ventricle	heart
48	chr4:95587800-95598400	Weak transcription	HSMM	muscle
49	chr4:95588000-95598400	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr4:95588000-95599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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