Variant report

Variant	rs2555216
Chromosome Location	chr4:95415446-95415447
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95413064..95415456-chr4:95417034..95419841,2	K562	blood:
2	chr4:95375609..95377732-chr4:95414007..95416782,2	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1082514	0.94[ASN][1000 genomes]
rs17378658	0.88[EUR][1000 genomes]
rs17379209	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2639793	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2639795	0.83[EUR][1000 genomes]
rs28502775	0.88[EUR][1000 genomes]
rs35793531	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3805301	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002911	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs699861	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73833924	0.94[ASN][1000 genomes]
rs774983	1.00[ASN][1000 genomes]
rs774988	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774989	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774993	0.88[EUR][1000 genomes];0.94[ASN][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
rs2555216	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 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	chr4:95387400-95420800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:95394400-95419200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:95394400-95428000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:95396600-95419000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:95398400-95428400	Weak transcription	Small Intestine	intestine
7	chr4:95400800-95440000	Weak transcription	Lung	lung
8	chr4:95401800-95420800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:95402000-95416800	Weak transcription	Pancreas	Pancrea
10	chr4:95403000-95416600	Weak transcription	Left Ventricle	heart
11	chr4:95403800-95417800	Weak transcription	HepG2	liver
12	chr4:95405000-95429000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:95406000-95419800	Weak transcription	GM12878-XiMat	blood
14	chr4:95407200-95428000	Weak transcription	Placenta	Placenta
15	chr4:95408000-95428000	Weak transcription	K562	blood
16	chr4:95408200-95422000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:95409000-95422000	Weak transcription	Ovary	ovary
18	chr4:95409400-95419000	Weak transcription	Aorta	Aorta
19	chr4:95410200-95416000	Weak transcription	Fetal Intestine Large	intestine
20	chr4:95410200-95422000	Weak transcription	Right Atrium	heart
21	chr4:95411000-95427800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:95412200-95416200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:95412400-95416600	Weak transcription	Right Ventricle	heart
24	chr4:95412400-95422000	Weak transcription	Liver	Liver
25	chr4:95412400-95424600	Weak transcription	Colon Smooth Muscle	Colon
26	chr4:95412800-95426000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:95412800-95428400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:95413000-95426200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:95413200-95417800	Weak transcription	Stomach Mucosa	stomach
30	chr4:95413200-95418200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:95413200-95427400	Weak transcription	A549	lung
32	chr4:95413200-95428000	Weak transcription	Hela-S3	cervix
33	chr4:95413400-95419200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:95413400-95425800	Weak transcription	HSMMtube	muscle
35	chr4:95413400-95428000	Weak transcription	NH-A	brain
36	chr4:95413400-95428400	Weak transcription	NHLF	lung
37	chr4:95413600-95416600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr4:95413600-95418000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:95413600-95418200	Weak transcription	NHEK	skin
40	chr4:95413600-95421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:95413600-95425600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:95413800-95415600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:95413800-95416400	Weak transcription	Fetal Heart	heart
44	chr4:95413800-95417200	Strong transcription	HSMM	muscle
45	chr4:95413800-95417600	Strong transcription	Osteobl	bone
46	chr4:95413800-95418800	Weak transcription	HMEC	breast
47	chr4:95414200-95417200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:95414600-95429000	Weak transcription	Esophagus	oesophagus
49	chr4:95414800-95417200	Strong transcription	HUVEC	blood vessel
50	chr4:95414800-95419000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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