Variant report

Variant	rs2510778
Chromosome Location	chr4:95458450-95458451
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95456523..95459012-chr4:95469903..95471763,2	MCF-7	breast:
2	chr4:95457924..95459634-chr4:95461855..95464045,2	K562	blood:
3	chr4:95458379..95460078-chr4:95465243..95467289,2	K562	blood:
4	chr4:95455418..95457640-chr4:95458337..95460219,4	K562	blood:
5	chr4:95455791..95459041-chr4:95471671..95474537,3	K562	blood:
6	chr4:95371767..95374402-chr4:95456594..95458553,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203436	Chromatin interaction
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12510147	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs1353044	0.94[CEU][hapmap]
rs1493112	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2162346	0.81[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2433317	0.89[CEU][hapmap]
rs2433324	0.84[CEU][hapmap]
rs2433325	0.94[CEU][hapmap]
rs2438142	0.89[CEU][hapmap]
rs2438144	0.94[CEU][hapmap]
rs2452565	0.94[CEU][hapmap]
rs2452578	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs2452583	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2452597	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2452598	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2452600	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2510767	0.82[CHB][hapmap]
rs2510770	0.84[ASN][1000 genomes]
rs2510773	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2510785	0.94[CEU][hapmap]
rs2510786	0.94[CEU][hapmap]
rs2510787	0.84[CEU][hapmap]
rs2510788	0.94[CEU][hapmap]
rs2510795	0.89[CEU][hapmap]
rs2577056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3133150	0.80[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.90[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
rs2510778	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 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	chr4:95442000-95469600	Weak transcription	Primary T cells from cord blood	blood
3	chr4:95449200-95470200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:95449800-95460400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:95450400-95465800	Weak transcription	Lung	lung
6	chr4:95450600-95459600	Weak transcription	Brain Angular Gyrus	brain
7	chr4:95453800-95459400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:95453800-95459600	Weak transcription	NHDF-Ad	bronchial
9	chr4:95453800-95460400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr4:95453800-95465400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:95454400-95459000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr4:95454600-95460200	Enhancers	Colon Smooth Muscle	Colon
13	chr4:95454600-95462600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr4:95455000-95459000	Enhancers	Adipose Nuclei	Adipose
15	chr4:95455400-95458800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:95455600-95460000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:95455800-95460200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:95456000-95459600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr4:95456200-95463200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr4:95456400-95459600	Enhancers	A549	lung
21	chr4:95456400-95460600	Weak transcription	NHEK	skin
22	chr4:95456400-95462800	Enhancers	HSMMtube	muscle
23	chr4:95456600-95459800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr4:95456600-95460200	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr4:95456600-95460800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:95456800-95460800	Weak transcription	HMEC	breast
27	chr4:95456800-95465000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:95456800-95469800	Weak transcription	Ovary	ovary
29	chr4:95456800-95470200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:95457000-95459600	Enhancers	HSMM	muscle
31	chr4:95457000-95469800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:95457200-95459600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:95457200-95459800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr4:95457200-95460000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:95457400-95459600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:95457400-95459600	Weak transcription	Aorta	Aorta
37	chr4:95457400-95459600	Weak transcription	Psoas Muscle	Psoas
38	chr4:95457400-95459800	Enhancers	Stomach Mucosa	stomach
39	chr4:95457400-95459800	Enhancers	Osteobl	bone
40	chr4:95457400-95461400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:95457400-95461600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr4:95457400-95462000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:95457400-95462800	Weak transcription	Left Ventricle	heart
44	chr4:95457400-95465800	Weak transcription	Pancreas	Pancrea
45	chr4:95457400-95469800	Weak transcription	Fetal Muscle Leg	muscle
46	chr4:95457400-95470000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:95457400-95485400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr4:95457600-95459000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:95457600-95465600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:95457800-95459400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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