Variant report

Variant	rs2280003
Chromosome Location	chr4:95575601-95575602
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:95568509..95570447-chr4:95573934..95576032,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10015716	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1043848	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10590	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12500116	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12505788	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510147	0.85[CEU][hapmap]
rs12511169	1.00[ASW][hapmap];0.87[CEU][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13121500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509620	0.85[LWK][hapmap]
rs17021918	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17021972	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2136486	0.87[CEU][hapmap];0.93[EUR][1000 genomes]
rs2452592	0.81[EUR][1000 genomes]
rs2452597	0.81[CEU][hapmap]
rs2452598	0.81[CEU][hapmap]
rs2452600	0.81[CEU][hapmap]
rs2510767	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs35964087	0.94[EUR][1000 genomes]
rs3762876	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61597100	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6817664	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6822544	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6837308	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659399	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674144	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7681843	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7694162	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998071	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2280003	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL
rs2280003	PDLIM5	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
2	chr4:95525000-95586400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr4:95525000-95590000	Weak transcription	Lung	lung
4	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
5	chr4:95533800-95594200	Weak transcription	Gastric	stomach
6	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
7	chr4:95538000-95585200	Weak transcription	Colonic Mucosa	Colon
8	chr4:95538200-95582600	Weak transcription	Hela-S3	cervix
9	chr4:95538200-95586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:95538600-95587000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr4:95540000-95587000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
14	chr4:95541400-95580200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:95543000-95586000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr4:95543000-95586400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:95549000-95586600	Weak transcription	Brain Hippocampus Middle	brain
18	chr4:95555200-95578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:95555200-95581800	Weak transcription	Ovary	ovary
20	chr4:95557200-95588600	Weak transcription	GM12878-XiMat	blood
21	chr4:95557400-95583800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:95557800-95586200	Weak transcription	Thymus	Thymus
23	chr4:95558200-95580800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:95559000-95590200	Weak transcription	Right Ventricle	heart
25	chr4:95559600-95578200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:95561400-95585200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr4:95561600-95580200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:95562600-95578200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr4:95563200-95584400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:95563600-95578200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:95563600-95578400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:95563600-95583400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:95563600-95589000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:95563800-95579400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:95563800-95583400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:95563800-95583400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:95564000-95578400	Weak transcription	NHEK	skin
38	chr4:95564000-95581200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:95564000-95587000	Weak transcription	NHLF	lung
40	chr4:95564000-95595000	Weak transcription	NHDF-Ad	bronchial
41	chr4:95567800-95582200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:95567800-95587400	Weak transcription	HepG2	liver
43	chr4:95568200-95578200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:95568400-95578200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:95568400-95578400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:95570000-95581800	Weak transcription	Esophagus	oesophagus
47	chr4:95570400-95576600	Strong transcription	HSMMtube	muscle
48	chr4:95570400-95581000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:95570600-95576600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:95570800-95578200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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