Variant report

Variant	rs7656545
Chromosome Location	chr4:95569216-95569217
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95568169..95569677-chr4:95571228..95573949,2	K562	blood:
2	chr4:95566714..95569669-chr4:95570638..95572728,2	K562	blood:
3	chr4:95568509..95570447-chr4:95573934..95576032,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10010013	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10014050	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10025074	0.82[CHB][hapmap]
rs10025288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10213504	0.82[CHB][hapmap]
rs1043862	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056772	1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097431	0.94[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs11097432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134984	0.83[EUR][1000 genomes]
rs11550270	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726587	0.82[CHB][hapmap]
rs11731606	0.82[CHB][hapmap]
rs11735212	1.00[CHB][hapmap]
rs12294	0.81[EUR][1000 genomes]
rs12331809	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331835	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331920	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509617	0.83[EUR][1000 genomes]
rs17021981	0.86[AMR][1000 genomes]
rs17336353	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs1802345	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452593	0.82[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs2452594	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs28376560	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376694	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28582311	0.86[EUR][1000 genomes]
rs28654759	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28709926	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805271	0.84[EUR][1000 genomes]
rs3805272	0.84[EUR][1000 genomes]
rs3805274	0.82[CHB][hapmap]
rs3805283	0.82[CHB][hapmap]
rs3805286	0.82[CHB][hapmap]
rs3828518	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs4590045	0.81[EUR][1000 genomes]
rs6816687	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs6830074	0.82[CHB][hapmap]
rs6840428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679284	1.00[CHB][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7656545	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 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	chr4:95497200-95569400	Weak transcription	Esophagus	oesophagus
3	chr4:95525000-95569600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:95525000-95586400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:95525000-95590000	Weak transcription	Lung	lung
6	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
7	chr4:95533800-95594200	Weak transcription	Gastric	stomach
8	chr4:95537600-95573400	Weak transcription	Spleen	Spleen
9	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
10	chr4:95538000-95585200	Weak transcription	Colonic Mucosa	Colon
11	chr4:95538200-95582600	Weak transcription	Hela-S3	cervix
12	chr4:95538200-95586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:95538600-95587000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr4:95540000-95587000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:95540400-95570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:95541000-95572600	Weak transcription	Small Intestine	intestine
18	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
19	chr4:95541400-95580200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:95541600-95571400	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:95543000-95586000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:95543000-95586400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:95547800-95573000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:95549000-95586600	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:95555200-95578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:95555200-95581800	Weak transcription	Ovary	ovary
27	chr4:95557200-95570600	Weak transcription	Fetal Intestine Small	intestine
28	chr4:95557200-95588600	Weak transcription	GM12878-XiMat	blood
29	chr4:95557400-95569800	Weak transcription	Fetal Heart	heart
30	chr4:95557400-95583800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:95557800-95586200	Weak transcription	Thymus	Thymus
32	chr4:95558200-95580800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:95559000-95590200	Weak transcription	Right Ventricle	heart
34	chr4:95559600-95578200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:95560800-95569600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:95561200-95571600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:95561400-95571400	Weak transcription	Aorta	Aorta
38	chr4:95561400-95585200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr4:95561600-95580200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr4:95562400-95570600	Weak transcription	Colon Smooth Muscle	Colon
41	chr4:95562600-95578200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:95563200-95584400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:95563400-95571800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:95563600-95578200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:95563600-95578400	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr4:95563600-95583400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr4:95563600-95589000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:95563800-95571800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr4:95563800-95574200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr4:95563800-95579400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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