Variant report

Variant	rs8042458
Chromosome Location	chr15:50164149-50164150
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	chr15:50158299..50161913-chr15:50163926..50167616,5	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1059850	0.84[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs1059851	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1059852	0.95[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs11070723	0.81[EUR][1000 genomes]
rs11070733	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11630021	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11632077	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11632116	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11633343	0.95[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11633465	0.91[EUR][1000 genomes]
rs11633470	1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs11633571	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs11633714	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs11633744	0.95[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs11633759	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11634914	0.86[EUR][1000 genomes]
rs11636769	0.85[EUR][1000 genomes]
rs11853881	1.00[JPT][hapmap]
rs12148168	0.81[EUR][1000 genomes]
rs12185124	0.84[AMR][1000 genomes]
rs12901108	0.82[EUR][1000 genomes]
rs12903153	0.86[EUR][1000 genomes]
rs12907836	0.91[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12909447	0.91[EUR][1000 genomes]
rs12914231	1.00[JPT][hapmap]
rs12915207	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs13329598	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16962994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes]
rs16962999	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17486097	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs17486425	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs17486446	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs17486544	0.86[EUR][1000 genomes]
rs17487811	1.00[JPT][hapmap]
rs2413975	1.00[JPT][hapmap]
rs28550208	0.82[AMR][1000 genomes]
rs28706888	0.83[AMR][1000 genomes]
rs34404202	0.87[EUR][1000 genomes]
rs34449112	0.85[EUR][1000 genomes]
rs34561282	0.81[EUR][1000 genomes]
rs34751824	0.81[EUR][1000 genomes]
rs34845057	0.95[EUR][1000 genomes]
rs35827271	0.85[EUR][1000 genomes]
rs35899336	0.81[EUR][1000 genomes]
rs35958858	0.81[EUR][1000 genomes]
rs4275793	0.86[EUR][1000 genomes]
rs4347574	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4494482	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4494483	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4544192	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61618346	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493383	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66809683	0.93[EUR][1000 genomes]
rs71469605	0.83[EUR][1000 genomes]
rs7170482	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7172553	0.90[EUR][1000 genomes]
rs7172585	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72733056	0.86[EUR][1000 genomes]
rs7497350	0.81[GIH][hapmap];1.00[JPT][hapmap]
rs8023895	0.85[EUR][1000 genomes]
rs8025533	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs8031452	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs8036570	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8038434	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8041979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][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
rs8042458	C15orf48	cis	parietal	SCAN
rs8042458	CATSPER2P1	cis	cerebellum	SCAN
rs8042458	EIF3J	cis	cerebellum	SCAN
rs8042458	CTDSPL2	cis	cerebellum	SCAN

Chromatin state (count:24 , 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	chr15:50138200-50189800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:50145600-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:50149400-50198000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr15:50156000-50168400	Weak transcription	Ovary	ovary
7	chr15:50158400-50167800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:50158800-50170600	Weak transcription	Placenta	Placenta
9	chr15:50159200-50168400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:50160600-50168600	Weak transcription	Hela-S3	cervix
11	chr15:50161600-50175600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr15:50161800-50179000	Strong transcription	Primary hematopoietic stem cells	blood
13	chr15:50161800-50210600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr15:50162200-50164600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:50162400-50172200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:50162800-50168600	Weak transcription	Fetal Kidney	kidney
17	chr15:50163000-50164200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:50163000-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:50163200-50164200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:50163600-50164200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:50163600-50164200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr15:50163600-50164200	Enhancers	Osteobl	bone
23	chr15:50163600-50164400	Strong transcription	Adipose Nuclei	Adipose
24	chr15:50163600-50164600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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