Variant report

Variant	rs2452593
Chromosome Location	chr4:95487714-95487715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10010013	0.85[EUR][1000 genomes]
rs10014050	0.87[EUR][1000 genomes]
rs10025074	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs10025288	0.84[TSI][hapmap]
rs10213504	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1043862	0.81[TSI][hapmap]
rs1056772	0.81[TSI][hapmap]
rs11097431	0.88[CEU][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11097432	0.85[TSI][hapmap]
rs11726587	1.00[CHB][hapmap]
rs11731606	1.00[CHB][hapmap]
rs17336353	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2452581	0.89[ASN][1000 genomes]
rs2452594	0.94[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2510766	0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs2510767	0.92[YRI][hapmap]
rs2510771	0.89[ASN][1000 genomes]
rs3805271	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805272	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805274	1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3805283	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs3805286	1.00[CHB][hapmap]
rs3828518	0.94[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4590045	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816687	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6830074	0.88[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.89[ASN][1000 genomes]
rs7285	0.85[TSI][hapmap]
rs7655928	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs7656545	0.82[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs7679284	0.82[CHB][hapmap]
rs9307144	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2452593	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95458200-95488800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:95463000-95487800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:95470000-95489200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:95470600-95489200	Weak transcription	Small Intestine	intestine
5	chr4:95479800-95491400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr4:95479800-95496800	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:95480600-95488000	Enhancers	Liver	Liver
8	chr4:95481200-95494600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:95481400-95496800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:95481400-95496800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:95483200-95488400	Enhancers	HUVEC	blood vessel
12	chr4:95483200-95488800	Weak transcription	K562	blood
13	chr4:95483400-95491600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:95483400-95491800	Weak transcription	Brain Anterior Caudate	brain
15	chr4:95483400-95496600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:95483400-95496800	Weak transcription	NHEK	skin
17	chr4:95483400-95524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:95483600-95496200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:95483800-95488800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:95483800-95491800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:95483800-95496600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:95483800-95496800	Weak transcription	Gastric	stomach
23	chr4:95483800-95497000	Weak transcription	HMEC	breast
24	chr4:95484000-95488600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:95484000-95488800	Weak transcription	Adipose Nuclei	Adipose
26	chr4:95484000-95488800	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:95484000-95489000	Weak transcription	Stomach Mucosa	stomach
28	chr4:95484000-95491400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:95484000-95495600	Weak transcription	NH-A	brain
30	chr4:95484000-95496600	Weak transcription	HSMMtube	muscle
31	chr4:95484000-95507400	Weak transcription	Hela-S3	cervix
32	chr4:95484600-95496800	Weak transcription	HSMM	muscle
33	chr4:95484800-95488800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:95485400-95488200	Enhancers	Fetal Heart	heart
35	chr4:95485600-95488800	Weak transcription	Right Atrium	heart
36	chr4:95485600-95496600	Weak transcription	Ovary	ovary
37	chr4:95485800-95488000	Enhancers	HepG2	liver
38	chr4:95485800-95488600	Weak transcription	Osteobl	bone
39	chr4:95485800-95488800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:95485800-95488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:95485800-95495200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr4:95485800-95496800	Weak transcription	Psoas Muscle	Psoas
43	chr4:95485800-95496800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr4:95486000-95489000	Weak transcription	Fetal Intestine Small	intestine
45	chr4:95486000-95496800	Weak transcription	Aorta	Aorta
46	chr4:95486200-95495000	Weak transcription	Placenta	Placenta
47	chr4:95486200-95495200	Weak transcription	Left Ventricle	heart
48	chr4:95486400-95493200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr4:95486800-95488800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr4:95486800-95490400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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