Variant report

Variant	rs10025074
Chromosome Location	chr4:95474562-95474563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95474428..95476516-chr4:95479995..95482160,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10000208	0.87[EUR][1000 genomes]
rs10213504	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726587	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11731606	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12498904	0.87[ASN][1000 genomes]
rs17336353	0.82[CHB][hapmap]
rs2452581	1.00[ASN][1000 genomes]
rs2452593	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2452594	0.82[CHB][hapmap]
rs2510766	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510771	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28416638	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3792664	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs3805271	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3805272	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3805274	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805286	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs3805288	0.85[CEU][hapmap];0.82[YRI][hapmap]
rs3828518	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs6812098	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6816687	0.82[CHB][hapmap]
rs6830074	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656545	0.82[CHB][hapmap]
rs7679284	0.82[CHB][hapmap]
rs7683990	0.87[ASN][1000 genomes]
rs9307144	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10025074	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:95457400-95485400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:95458000-95480400	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:95458200-95483000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:95458200-95488800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:95459000-95480400	Weak transcription	Adipose Nuclei	Adipose
7	chr4:95459800-95481200	Weak transcription	Aorta	Aorta
8	chr4:95463000-95480400	Weak transcription	Right Ventricle	heart
9	chr4:95463000-95487800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:95463200-95481200	Weak transcription	Left Ventricle	heart
11	chr4:95466000-95474800	Weak transcription	Psoas Muscle	Psoas
12	chr4:95466000-95475000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:95467600-95479400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:95469800-95476600	Enhancers	Fetal Heart	heart
15	chr4:95470000-95489200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:95470400-95477800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:95470400-95479600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:95470400-95479600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:95470400-95480400	Weak transcription	NHLF	lung
20	chr4:95470400-95482600	Weak transcription	HepG2	liver
21	chr4:95470400-95484800	Weak transcription	Fetal Intestine Large	intestine
22	chr4:95470600-95479400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:95470600-95480800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:95470600-95483600	Weak transcription	Fetal Intestine Small	intestine
25	chr4:95470600-95489200	Weak transcription	Small Intestine	intestine
26	chr4:95470800-95479200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:95471000-95479200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr4:95471000-95480200	Weak transcription	HMEC	breast
29	chr4:95471000-95480400	Weak transcription	Hela-S3	cervix
30	chr4:95471000-95480600	Weak transcription	Placenta	Placenta
31	chr4:95471200-95480600	Weak transcription	Right Atrium	heart
32	chr4:95472400-95475000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:95472600-95481600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:95473000-95480400	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:95473200-95479200	Weak transcription	K562	blood
36	chr4:95473200-95479400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:95473200-95480400	Weak transcription	HSMMtube	muscle
38	chr4:95473400-95475200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:95473400-95475600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:95473400-95480600	Weak transcription	Liver	Liver
41	chr4:95473800-95479400	Weak transcription	NH-A	brain
42	chr4:95474000-95475800	Strong transcription	Osteobl	bone
43	chr4:95474000-95479600	Weak transcription	HSMM	muscle
44	chr4:95474000-95480200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:95474200-95474600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:95474200-95474600	Weak transcription	HUVEC	blood vessel
47	chr4:95474400-95475000	Strong transcription	NHEK	skin
48	chr4:95474400-95475400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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