Variant report

Variant	rs17486544
Chromosome Location	chr15:50145372-50145373
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	chr15:50138152..50141031-chr15:50143945..50145459,2	MCF-7	breast:
2	chr15:50144065..50146550-chr15:50148452..50150273,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10519242	0.82[AMR][1000 genomes]
rs1059850	0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs1059851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070723	0.89[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];0.91[ASN][1000 genomes]
rs11631995	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11632077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11633343	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11633465	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11633470	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11633571	1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[TSI][hapmap]
rs11633644	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11633714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633759	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11634082	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11634914	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636769	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11639332	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11853881	1.00[JPT][hapmap]
rs12148168	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12372951	0.81[EUR][1000 genomes]
rs12901108	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12902979	0.84[EUR][1000 genomes]
rs12903153	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903481	0.86[EUR][1000 genomes]
rs12904017	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12907836	0.95[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs12909447	0.88[AMR][1000 genomes];0.92[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];0.91[ASN][1000 genomes]
rs16962994	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs16962999	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17486097	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17486425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17486446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17486663	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17487811	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2413975	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34404202	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34449112	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34561282	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34751824	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34845057	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35827271	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35899336	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35958858	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4275793	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4347574	1.00[CEU][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4494482	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4494483	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4544192	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55967655	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61618346	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493383	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs66809683	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71469605	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7170482	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7172553	0.91[ASN][1000 genomes]
rs7172585	0.80[EUR][1000 genomes]
rs72733056	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7497350	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8023895	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8025169	1.00[YRI][hapmap]
rs8025533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8031452	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8036570	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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];0.86[EUR][1000 genomes]
rs8042458	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17486544	CATSPER2	cis	cerebellum	SCAN
rs17486544	CATSPER2P1	cis	cerebellum	SCAN
rs17486544	PPIP5K1	cis	parietal	SCAN
rs17486544	CTDSPL2	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50135200-50181400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:50135800-50187400	Weak transcription	Liver	Liver
3	chr15:50136600-50149000	Weak transcription	Placenta	Placenta
4	chr15:50138000-50146800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:50138200-50189800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:50140200-50155600	Weak transcription	Ovary	ovary
7	chr15:50141200-50148000	Weak transcription	Aorta	Aorta
8	chr15:50141200-50151600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:50141400-50147200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:50141400-50151200	Weak transcription	HSMM	muscle
11	chr15:50142400-50146600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:50142400-50147400	Weak transcription	Osteobl	bone
13	chr15:50142600-50145600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:50143600-50147000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:50144000-50146000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:50144200-50146400	Strong transcription	Adipose Nuclei	Adipose
17	chr15:50144400-50146000	ZNF genes & repeats	Hela-S3	cervix
18	chr15:50144400-50148600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:50144400-50159800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:50144600-50145400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr15:50144600-50145800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:50144600-50146000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:50145000-50145400	Enhancers	NHDF-Ad	bronchial
24	chr15:50145000-50146400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:50145000-50146800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr15:50145200-50146400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr15:50145200-50146400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr15:50145200-50146600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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