Variant report

Variant	rs3828518
Chromosome Location	chr4:95500628-95500629
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	chr4:95498533..95501686-chr4:95504980..95507488,3	K562	blood:
2	chr4:95373418..95376357-chr4:95500477..95502998,3	K562	blood:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10010013	0.89[EUR][1000 genomes]
rs10014050	0.90[EUR][1000 genomes]
rs10025074	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs10025288	0.85[CHB][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs10025410	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs10049504	0.85[CHB][hapmap]
rs10084920	0.85[ASN][1000 genomes]
rs10213504	0.82[CHB][hapmap]
rs1043862	0.81[CHD][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs1056772	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap]
rs11097431	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097432	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs11550270	0.80[EUR][1000 genomes]
rs11726587	0.82[CHB][hapmap]
rs11731606	0.82[CHB][hapmap]
rs11735212	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs12331809	0.81[EUR][1000 genomes]
rs12331835	0.81[EUR][1000 genomes]
rs12331920	0.81[EUR][1000 genomes]
rs17336353	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1802345	0.80[EUR][1000 genomes]
rs2452593	0.94[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2452594	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28376560	0.82[EUR][1000 genomes]
rs28376694	0.80[EUR][1000 genomes]
rs28654759	0.81[EUR][1000 genomes]
rs28709926	0.80[EUR][1000 genomes]
rs3805271	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3805272	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3805274	0.82[CHB][hapmap]
rs3805283	0.82[CHB][hapmap]
rs3805286	0.82[CHB][hapmap]
rs3805288	0.85[ASW][hapmap]
rs4590045	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6816687	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6830074	0.82[CHB][hapmap]
rs6840428	0.85[CHB][hapmap]
rs7285	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs7655928	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs7656545	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs7679284	1.00[CHB][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3828518	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95483400-95524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:95484000-95507400	Weak transcription	Hela-S3	cervix
3	chr4:95489000-95507400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr4:95489200-95506800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:95489200-95507400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:95489200-95509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:95489400-95506200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:95489600-95508200	Weak transcription	GM12878-XiMat	blood
9	chr4:95489600-95522800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr4:95489600-95539200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:95492000-95502200	Weak transcription	Fetal Intestine Small	intestine
12	chr4:95493200-95540200	Weak transcription	Small Intestine	intestine
13	chr4:95493200-95584800	Weak transcription	Primary B cells from cord blood	blood
14	chr4:95494000-95506200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:95495200-95506800	Weak transcription	Fetal Stomach	stomach
16	chr4:95496000-95501800	Weak transcription	Fetal Lung	lung
17	chr4:95497200-95506400	Weak transcription	Left Ventricle	heart
18	chr4:95497200-95506800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:95497200-95506800	Weak transcription	Psoas Muscle	Psoas
20	chr4:95497200-95507400	Weak transcription	Primary T cells from cord blood	blood
21	chr4:95497200-95511000	Weak transcription	Ovary	ovary
22	chr4:95497200-95512600	Weak transcription	Aorta	Aorta
23	chr4:95497200-95512600	Weak transcription	Pancreas	Pancrea
24	chr4:95497200-95513800	Weak transcription	Right Ventricle	heart
25	chr4:95497200-95516200	Weak transcription	Right Atrium	heart
26	chr4:95497200-95520000	Weak transcription	Spleen	Spleen
27	chr4:95497200-95524600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:95497200-95524600	Weak transcription	Gastric	stomach
29	chr4:95497200-95524600	Weak transcription	Lung	lung
30	chr4:95497200-95526000	Weak transcription	Brain Angular Gyrus	brain
31	chr4:95497200-95553000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:95497200-95569400	Weak transcription	Esophagus	oesophagus
33	chr4:95497400-95502400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr4:95497400-95505000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr4:95497400-95505000	Weak transcription	Brain Substantia Nigra	brain
36	chr4:95497400-95506000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:95497400-95506800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr4:95497400-95506800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr4:95497400-95506800	Weak transcription	Adipose Nuclei	Adipose
40	chr4:95497400-95507600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:95497400-95510200	Weak transcription	Fetal Kidney	kidney
42	chr4:95497400-95513600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:95497400-95515000	Weak transcription	Colonic Mucosa	Colon
44	chr4:95497400-95524200	Weak transcription	NHLF	lung
45	chr4:95497400-95526200	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:95497400-95542000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:95497600-95502200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr4:95497600-95505200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:95497600-95506600	Weak transcription	Placenta	Placenta
50	chr4:95497600-95506800	Weak transcription	Fetal Muscle Leg	muscle

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