Variant report

Variant	rs4275793
Chromosome Location	chr15:50150400-50150401
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	chr15:50147995..50150192-chr15:50150286..50152318,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10519242	0.81[EUR][1000 genomes]
rs10519250	1.00[LWK][hapmap]
rs1059850	0.86[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059851	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1059852	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070723	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11070733	0.85[EUR][1000 genomes]
rs11630021	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11631995	0.87[EUR][1000 genomes]
rs11632077	0.95[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]
rs11632116	0.95[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]
rs11633343	0.95[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11633465	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11633470	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11633571	1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs11633644	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11633714	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11633744	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11634082	0.80[EUR][1000 genomes]
rs11634914	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636769	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11639332	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11853881	1.00[JPT][hapmap]
rs12148168	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12185124	0.81[EUR][1000 genomes]
rs12593937	1.00[LWK][hapmap]
rs12901108	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12902979	0.82[EUR][1000 genomes]
rs12903153	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903481	0.83[EUR][1000 genomes]
rs12904017	0.87[EUR][1000 genomes]
rs12905883	1.00[LWK][hapmap]
rs12907836	0.91[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12909447	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12914231	1.00[JPT][hapmap]
rs12915207	1.00[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs13329598	1.00[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];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs16962999	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17486097	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17486425	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17486446	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17486544	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17486663	0.81[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]
rs28550208	0.81[EUR][1000 genomes]
rs28706888	0.80[EUR][1000 genomes]
rs34404202	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34449112	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34561282	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34751824	0.90[EUR][1000 genomes]
rs34845057	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35827271	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35899336	0.90[EUR][1000 genomes]
rs35958858	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4347574	0.95[CEU][hapmap];0.82[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs4494482	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4494483	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4544192	0.95[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55967655	0.90[EUR][1000 genomes]
rs61618346	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493383	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs66809683	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71469605	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7170482	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7172553	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7172585	0.80[EUR][1000 genomes]
rs72733056	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7497350	1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023895	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8025533	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8027073	1.00[LWK][hapmap]
rs8031452	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8036570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8038434	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs8041979	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs8042458	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4275793	C15orf48	cis	parietal	SCAN
rs4275793	CTDSPL2	cis	cerebellum	SCAN
rs4275793	CATSPER2	cis	cerebellum	SCAN
rs4275793	CATSPER2P1	cis	cerebellum	SCAN
rs4275793	EIF3J	cis	cerebellum	SCAN

Chromatin state (count:31 , 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	chr15:50140200-50155600	Weak transcription	Ovary	ovary
5	chr15:50141200-50151600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:50141400-50151200	Weak transcription	HSMM	muscle
7	chr15:50144400-50159800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:50145600-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:50146400-50151600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:50146400-50160000	Strong transcription	Primary hematopoietic stem cells	blood
11	chr15:50147200-50158400	Enhancers	NHDF-Ad	bronchial
12	chr15:50147400-50150400	Enhancers	NHLF	lung
13	chr15:50147400-50153400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:50147400-50153400	Enhancers	Osteobl	bone
15	chr15:50148800-50151000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:50149200-50151600	Weak transcription	Adipose Nuclei	Adipose
17	chr15:50149200-50152200	Weak transcription	Fetal Stomach	stomach
18	chr15:50149400-50151200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:50149400-50155400	Weak transcription	Placenta	Placenta
20	chr15:50149400-50198000	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:50149600-50151000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:50149600-50151800	Enhancers	A549	lung
23	chr15:50149600-50152200	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:50149600-50153400	Enhancers	Hela-S3	cervix
25	chr15:50149600-50153800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:50149600-50160600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:50149600-50160800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:50150000-50150800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr15:50150000-50155800	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr15:50150200-50151800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:50150400-50151200	Weak transcription	NHLF	lung

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