Variant report

Variant	rs28502775
Chromosome Location	chr4:95401945-95401946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95392600..95395263-chr4:95399484..95402281,2	K562	blood:
2	chr4:95372993..95375546-chr4:95399640..95402667,3	K562	blood:
3	chr4:95391486..95396177-chr4:95398178..95402962,4	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17378658	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17379209	0.89[EUR][1000 genomes]
rs2555216	0.88[EUR][1000 genomes]
rs2639793	0.89[EUR][1000 genomes]
rs3805301	0.89[EUR][1000 genomes]
rs5002911	0.80[EUR][1000 genomes]
rs7670371	0.88[AMR][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	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28502775	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95375000-95440200	Weak transcription	Primary T cells from cord blood	blood
2	chr4:95387400-95410000	Weak transcription	NHLF	lung
3	chr4:95387400-95420800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:95389600-95406000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:95393800-95405600	Weak transcription	HSMMtube	muscle
6	chr4:95394000-95405000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:95394200-95404800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:95394400-95405800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:95394400-95407000	Weak transcription	NH-A	brain
10	chr4:95394400-95407800	Weak transcription	Aorta	Aorta
11	chr4:95394400-95419200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:95394400-95428000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:95394600-95406000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:95395400-95405000	Weak transcription	HSMM	muscle
15	chr4:95396600-95419000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr4:95396800-95410000	Weak transcription	Fetal Intestine Large	intestine
17	chr4:95398400-95407600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:95398400-95408800	Weak transcription	Brain Substantia Nigra	brain
19	chr4:95398400-95428400	Weak transcription	Small Intestine	intestine
20	chr4:95398600-95403400	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:95398600-95405800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr4:95399000-95404600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:95399000-95409800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:95399600-95402000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr4:95399600-95404200	Enhancers	Fetal Heart	heart
26	chr4:95399800-95402200	Enhancers	A549	lung
27	chr4:95400000-95402000	Enhancers	K562	blood
28	chr4:95400200-95402000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr4:95400200-95402000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:95400200-95404000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr4:95400400-95402000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:95400400-95402000	Enhancers	Liver	Liver
33	chr4:95400400-95403400	Weak transcription	Fetal Intestine Small	intestine
34	chr4:95400400-95415200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:95400600-95402000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr4:95400600-95402000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr4:95400600-95402200	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr4:95400800-95402000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:95400800-95402200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:95400800-95405800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:95400800-95440000	Weak transcription	Lung	lung
42	chr4:95401000-95402000	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr4:95401000-95402400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr4:95401200-95402000	Enhancers	Rectal Smooth Muscle	rectum
45	chr4:95401200-95402200	Enhancers	Adipose Nuclei	Adipose
46	chr4:95401400-95402000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:95401400-95402000	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr4:95401400-95402000	Enhancers	Pancreas	Pancrea
49	chr4:95401400-95402200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:95401400-95403000	Enhancers	Left Ventricle	heart

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