Variant report

Variant	rs8025533
Chromosome Location	chr15:50138224-50138225
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50137595..50140472-chr15:50174008..50176378,2	K562	blood:
2	chr15:50138152..50141031-chr15:50143945..50145459,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10519250	1.00[LWK][hapmap]
rs1059850	0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs1059851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070723	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11070733	0.82[EUR][1000 genomes]
rs11630021	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631995	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11632077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633343	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11633465	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11633470	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11633571	1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap]
rs11633644	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11633714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11633759	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634082	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11634914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636769	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639332	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11853881	1.00[JPT][hapmap]
rs12148168	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12372951	0.82[EUR][1000 genomes]
rs12593937	1.00[LWK][hapmap]
rs12901108	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12902979	0.85[EUR][1000 genomes]
rs12903153	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12903481	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12904017	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12905883	1.00[LWK][hapmap]
rs12907836	0.95[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs12909447	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12914231	1.00[JPT][hapmap]
rs12915207	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs13329598	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962994	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs16962999	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs17486097	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17486425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17486446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17486544	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17486663	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17487811	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2413975	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34404202	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34449112	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34561282	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34751824	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34845057	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35827271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35899336	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35958858	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4275793	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4347574	1.00[CEU][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs4494482	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs4494483	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs4544192	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs55967655	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61618346	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493383	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs66809683	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71469605	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7170482	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs7172553	1.00[ASN][1000 genomes]
rs72733056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7497350	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8023895	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8027073	1.00[LWK][hapmap]
rs8031452	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.91[ASN][1000 genomes]
rs8036570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038434	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs8041979	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs8042458	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv833003	chr15:50100372-50273309	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8025533	CATSPER2P1	cis	cerebellum	SCAN
rs8025533	PPIP5K1	cis	parietal	SCAN
rs8025533	CTDSPL2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50124800-50139200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:50130800-50138400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr15:50132400-50141200	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:50134400-50140200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:50134600-50139600	Weak transcription	Ovary	ovary
6	chr15:50134800-50140200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:50135000-50139000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:50135200-50181400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:50135400-50139600	Weak transcription	HSMMtube	muscle
10	chr15:50135800-50187400	Weak transcription	Liver	Liver
11	chr15:50136400-50139000	Weak transcription	Osteobl	bone
12	chr15:50136600-50139000	Weak transcription	A549	lung
13	chr15:50136600-50139400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:50136600-50149000	Weak transcription	Placenta	Placenta
15	chr15:50137000-50138800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:50137000-50139000	Weak transcription	Adipose Nuclei	Adipose
17	chr15:50137600-50139000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:50137600-50139000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:50137800-50139600	Weak transcription	Colonic Mucosa	Colon
20	chr15:50137800-50141600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr15:50138000-50146800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr15:50138200-50138800	Weak transcription	Hela-S3	cervix
23	chr15:50138200-50142600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:50138200-50145200	Strong transcription	Primary hematopoietic stem cells	blood
25	chr15:50138200-50189800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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