Variant report

Variant	rs11630021
Chromosome Location	chr15:50158695-50158696
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50140531..50141322-chr15:50158499..50159411,2	MCF-7	breast:
2	chr15:50155057..50157653-chr15:50158605..50160734,2	K562	blood:
3	chr15:50115862..50118936-chr15:50156885..50160931,3	MCF-7	breast:
4	chr15:50157609..50159636-chr15:50284420..50286036,2	MCF-7	breast:
5	chr15:50158299..50161913-chr15:50163926..50167616,5	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1059850	0.85[ASW][hapmap];0.84[GIH][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.91[ASN][1000 genomes]
rs1059851	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1059852	0.95[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11070723	0.81[EUR][1000 genomes]
rs11070733	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11632077	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632116	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633343	0.95[CEU][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs11633465	0.91[EUR][1000 genomes]
rs11633470	0.91[EUR][1000 genomes]
rs11633571	0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs11633714	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633744	0.95[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11633759	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634914	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636769	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639332	0.80[EUR][1000 genomes]
rs11853881	1.00[JPT][hapmap]
rs12148168	0.81[EUR][1000 genomes]
rs12901108	0.83[EUR][1000 genomes]
rs12903153	0.85[EUR][1000 genomes]
rs12907836	0.91[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs12909447	0.91[EUR][1000 genomes]
rs12914231	1.00[JPT][hapmap]
rs12915207	0.83[CEU][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs13329598	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16962994	1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap]
rs16962999	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs17486097	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs17486425	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17486446	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]
rs17486544	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17486663	0.91[ASN][1000 genomes]
rs17487811	1.00[JPT][hapmap]
rs2413975	1.00[JPT][hapmap]
rs28550208	0.81[AMR][1000 genomes]
rs34404202	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34449112	0.85[EUR][1000 genomes]
rs34561282	0.81[EUR][1000 genomes]
rs34751824	0.81[EUR][1000 genomes]
rs34845057	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35827271	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35899336	0.81[EUR][1000 genomes]
rs35958858	0.81[EUR][1000 genomes]
rs4275793	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4347574	0.95[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4494482	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4494483	0.95[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4544192	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55967655	0.81[EUR][1000 genomes]
rs61618346	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493383	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs66809683	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71469605	0.83[EUR][1000 genomes]
rs7170482	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs7172553	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172585	0.91[EUR][1000 genomes]
rs72733056	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7497350	0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8023895	0.85[EUR][1000 genomes]
rs8025533	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]
rs8031452	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8036570	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038434	0.85[ASW][hapmap];0.95[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs8041979	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8042458	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]

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
rs11630021	C15orf48	cis	parietal	SCAN
rs11630021	EIF3J	cis	cerebellum	SCAN
rs11630021	CTDSPL2	cis	cerebellum	SCAN
rs11630021	CATSPER2P1	cis	cerebellum	SCAN

Chromatin state (count:21 , 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	chr15:50144400-50159800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:50145600-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:50146400-50160000	Strong transcription	Primary hematopoietic stem cells	blood
7	chr15:50149400-50198000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:50149600-50160600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:50149600-50160800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:50156000-50158800	Weak transcription	Aorta	Aorta
11	chr15:50156000-50168400	Weak transcription	Ovary	ovary
12	chr15:50157200-50158800	Enhancers	Placenta	Placenta
13	chr15:50157200-50160600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr15:50157600-50158800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:50157600-50158800	Strong transcription	Adipose Nuclei	Adipose
16	chr15:50157600-50159200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:50157800-50159200	Flanking Active TSS	A549	lung
18	chr15:50158000-50158800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:50158400-50167800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:50158600-50158800	Flanking Active TSS	Hela-S3	cervix
21	chr15:50158600-50160200	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links