Variant report

Variant	rs2568532
Chromosome Location	chr15:34387365-34387366
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:34379930..34382933-chr15:34385055..34387816,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11072954	0.93[EUR][1000 genomes]
rs11634597	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11853879	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11856158	1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs12592547	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs12592856	0.85[EUR][1000 genomes]
rs12594048	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs12903028	0.85[EUR][1000 genomes]
rs1436923	0.88[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16958770	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865925	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339374	0.85[EUR][1000 genomes]
rs2576308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576310	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28376576	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3794593	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4288968	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4468578	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4780214	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4780215	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4780216	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs522397	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs56310728	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57205845	0.85[ASN][1000 genomes]
rs623941	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6495519	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7161835	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7163226	0.96[EUR][1000 genomes]
rs7182085	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs721122	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73374335	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028703	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038259	1.00[CEU][hapmap];0.94[EUR][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	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1035579	chr15:34363159-34501115	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2568532	PGBD4	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34358600-34393000	Weak transcription	Aorta	Aorta
2	chr15:34368000-34391600	Weak transcription	Right Ventricle	heart
3	chr15:34368800-34392400	Weak transcription	Psoas Muscle	Psoas
4	chr15:34369600-34391600	Weak transcription	NHEK	skin
5	chr15:34372800-34393200	Weak transcription	Colonic Mucosa	Colon
6	chr15:34373600-34392400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:34374200-34392800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:34374400-34391600	Weak transcription	Fetal Brain Male	brain
9	chr15:34374800-34391600	Weak transcription	Small Intestine	intestine
10	chr15:34374800-34393000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:34375000-34392800	Weak transcription	Fetal Heart	heart
12	chr15:34375000-34393000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:34375400-34388800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:34375400-34388800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:34375600-34389000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:34375800-34391600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr15:34376000-34390200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:34376000-34392800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr15:34376800-34392400	Weak transcription	Brain Substantia Nigra	brain
20	chr15:34378400-34392400	Weak transcription	NHLF	lung
21	chr15:34378600-34392200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:34378600-34392600	Weak transcription	Fetal Kidney	kidney
23	chr15:34378800-34393000	Weak transcription	Lung	lung
24	chr15:34379000-34393000	Weak transcription	Esophagus	oesophagus
25	chr15:34380200-34391600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:34380200-34391800	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:34380200-34392800	Weak transcription	HSMMtube	muscle
28	chr15:34380200-34393000	Weak transcription	Ovary	ovary
29	chr15:34380200-34393400	Weak transcription	Gastric	stomach
30	chr15:34380400-34391600	Weak transcription	Thymus	Thymus
31	chr15:34380400-34391800	Weak transcription	Left Ventricle	heart
32	chr15:34380400-34391800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:34380400-34391800	Weak transcription	Spleen	Spleen
34	chr15:34380400-34392400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:34380600-34391800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:34381000-34390200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:34381200-34391600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:34381200-34393400	Weak transcription	Pancreas	Pancrea
39	chr15:34381400-34388800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:34382200-34392200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:34382400-34391600	Weak transcription	HepG2	liver
42	chr15:34382600-34391600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr15:34382600-34391600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:34382600-34392800	Weak transcription	Fetal Muscle Leg	muscle
45	chr15:34382800-34387400	Weak transcription	HMEC	breast
46	chr15:34383400-34391600	Weak transcription	Brain Angular Gyrus	brain
47	chr15:34384400-34388800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr15:34384600-34388800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:34384800-34388600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:34384800-34388800	Strong transcription	Primary T cells fromperipheralblood	blood

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