Variant report

Variant	rs2452578
Chromosome Location	chr4:95473162-95473163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95466562..95469843-chr4:95470075..95473924,5	K562	blood:
2	chr4:95455791..95459041-chr4:95471671..95474537,3	K562	blood:
3	chr4:95464708..95469426-chr4:95470140..95474023,5	K562	blood:
4	chr4:95373076..95374774-chr4:95472504..95474063,2	MCF-7	breast:
5	chr4:95386864..95390124-chr4:95470356..95473538,3	K562	blood:
6	chr4:95472261..95474248-chr4:95480587..95483073,2	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10033326	0.82[CHB][hapmap]
rs10034824	0.81[CHB][hapmap]
rs12500426	0.86[CHB][hapmap]
rs12510147	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1493112	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2162346	0.85[CHB][hapmap]
rs2452009	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452580	0.80[CHB][hapmap]
rs2452583	0.86[ASN][1000 genomes]
rs2452591	0.87[ASN][1000 genomes]
rs2452592	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2452597	0.95[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2452598	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2452599	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2452600	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2510767	0.83[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2510769	0.82[CHB][hapmap]
rs2510770	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2510772	0.80[CHB][hapmap]
rs2510773	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2510778	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs2577056	0.81[CEU][hapmap];0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs3133150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35044129	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3805263	0.81[CHB][hapmap]
rs3805266	0.86[CHB][hapmap]
rs3843444	0.86[CHB][hapmap]
rs4634230	0.86[CHB][hapmap]
rs4699312	0.86[CHB][hapmap]
rs4699540	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66542996	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6845201	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6854173	0.82[CHB][hapmap]
rs7662466	0.86[CHB][hapmap]
rs7682375	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs902981	0.82[CHB][hapmap]
rs9684901	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[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
rs2452578	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

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	chr4:95470400-95473200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:95470400-95473200	Enhancers	HSMMtube	muscle
18	chr4:95470400-95477800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:95470400-95479600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:95470400-95479600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:95470400-95480400	Weak transcription	NHLF	lung
22	chr4:95470400-95482600	Weak transcription	HepG2	liver
23	chr4:95470400-95484800	Weak transcription	Fetal Intestine Large	intestine
24	chr4:95470600-95473200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:95470600-95479400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:95470600-95480800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:95470600-95483600	Weak transcription	Fetal Intestine Small	intestine
28	chr4:95470600-95489200	Weak transcription	Small Intestine	intestine
29	chr4:95470800-95474400	Weak transcription	NHEK	skin
30	chr4:95470800-95479200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:95471000-95479200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:95471000-95480200	Weak transcription	HMEC	breast
33	chr4:95471000-95480400	Weak transcription	Hela-S3	cervix
34	chr4:95471000-95480600	Weak transcription	Placenta	Placenta
35	chr4:95471200-95480600	Weak transcription	Right Atrium	heart
36	chr4:95471400-95473200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:95471400-95473800	Enhancers	Osteobl	bone
38	chr4:95471600-95473200	Genic enhancers	HSMM	muscle
39	chr4:95472400-95475000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:95472600-95473200	Enhancers	A549	lung
41	chr4:95472600-95473400	Enhancers	Liver	Liver
42	chr4:95472600-95473600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:95472600-95473800	Enhancers	NH-A	brain
44	chr4:95472600-95481600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:95472800-95473200	Genic enhancers	K562	blood
46	chr4:95472800-95473400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr4:95472800-95473400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:95472800-95473400	Enhancers	NHDF-Ad	bronchial
49	chr4:95472800-95474000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:95472800-95474000	Enhancers	Muscle Satellite Cultured Cells	--

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