Variant report

Variant	rs17021918
Chromosome Location	chr4:95562877-95562878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10015716	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1043848	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10590	0.84[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12500116	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12505788	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12510147	0.85[CEU][hapmap]
rs12511169	0.92[ASW][hapmap];0.87[CEU][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13121500	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1509620	0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.80[ASN][1000 genomes]
rs17021972	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2136486	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs2280003	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]
rs2452591	0.81[EUR][1000 genomes]
rs2452592	0.83[EUR][1000 genomes]
rs2452597	0.81[CEU][hapmap]
rs2452598	0.81[CEU][hapmap]
rs2452600	0.81[CEU][hapmap]
rs2510767	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs35964087	0.92[EUR][1000 genomes]
rs3762876	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4699316	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61597100	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6817664	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6822544	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6837308	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7659399	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7674144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7681843	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7694162	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs998071	0.92[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][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	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

Variant related diseases (count:1)

Disease	PMID	Source
Prostate cancer	19767753	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17021918	PDLIM5	cis	parietal	SCAN

Chromatin state (count:92 , 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	chr4:95537000-95563000	Weak transcription	K562	blood
9	chr4:95537600-95573400	Weak transcription	Spleen	Spleen
10	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
11	chr4:95538000-95585200	Weak transcription	Colonic Mucosa	Colon
12	chr4:95538200-95582600	Weak transcription	Hela-S3	cervix
13	chr4:95538200-95586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:95538600-95587000	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr4:95540000-95566800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr4:95540000-95587000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:95540400-95570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:95541000-95572600	Weak transcription	Small Intestine	intestine
20	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
21	chr4:95541400-95580200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:95541600-95571400	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:95543000-95586000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:95543000-95586400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:95547800-95573000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:95549000-95586600	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:95551200-95563600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:95555200-95566600	Weak transcription	Fetal Intestine Large	intestine
29	chr4:95555200-95578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:95555200-95581800	Weak transcription	Ovary	ovary
31	chr4:95557000-95564200	Weak transcription	Psoas Muscle	Psoas
32	chr4:95557200-95563000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:95557200-95570600	Weak transcription	Fetal Intestine Small	intestine
34	chr4:95557200-95588600	Weak transcription	GM12878-XiMat	blood
35	chr4:95557400-95569800	Weak transcription	Fetal Heart	heart
36	chr4:95557400-95583800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:95557800-95586200	Weak transcription	Thymus	Thymus
38	chr4:95558000-95568600	Strong transcription	Placenta	Placenta
39	chr4:95558200-95580800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr4:95558800-95563400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr4:95559000-95590200	Weak transcription	Right Ventricle	heart
42	chr4:95559200-95564000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr4:95559600-95578200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:95560000-95564600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:95560200-95564000	Genic enhancers	HUVEC	blood vessel
46	chr4:95560200-95564200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr4:95560400-95564000	Strong transcription	Adipose Nuclei	Adipose
48	chr4:95560400-95568000	Strong transcription	Liver	Liver
49	chr4:95560800-95565200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr4:95560800-95569600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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