Variant report

Variant	rs1372548
Chromosome Location	chr3:19480313-19480314
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	chr2:105766716..105768972-chr3:19479211..19481306,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10514672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10514673	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1348231	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs1372551	1.00[CEU][hapmap]
rs1442199	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17005936	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17005937	1.00[CEU][hapmap]
rs17005949	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs17005954	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17005967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17005972	1.00[CEU][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17005976	1.00[CEU][hapmap];0.88[LWK][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes]
rs17005980	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17005983	1.00[CEU][hapmap]
rs17005985	1.00[CEU][hapmap]
rs17005998	1.00[CEU][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17006003	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17006010	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17006048	1.00[CEU][hapmap];0.82[MEX][hapmap]
rs4021207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs57565118	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57684768	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58915529	1.00[EUR][1000 genomes]
rs60546560	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60942804	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6776448	1.00[CEU][hapmap]
rs6796647	1.00[CEU][hapmap];0.90[CHD][hapmap]
rs6800537	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[MEX][hapmap]
rs6801951	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs7617994	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[MEX][hapmap]
rs951678	1.00[CEU][hapmap];0.82[MEX][hapmap];0.86[EUR][1000 genomes]
rs9841624	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517847	chr3:18845347-19483695	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1010123	chr3:18990307-19989504	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1004602	chr3:19031671-19930052	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv536511	chr3:19031671-19930052	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv948636	chr3:19335802-19856585	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv589855	chr3:19409153-19512074	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3386719	chr3:19454588-19895807	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19473000-19491400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:19474400-19513200	Weak transcription	Brain Germinal Matrix	brain
3	chr3:19474600-19482000	Weak transcription	Fetal Brain Male	brain
4	chr3:19478400-19481200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:19478800-19487600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:19479000-19481000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:19479200-19484400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:19479400-19488000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:19479600-19483000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:19479600-19483600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:19479800-19480400	Strong transcription	Brain Hippocampus Middle	brain
12	chr3:19479800-19480600	Strong transcription	Brain Cingulate Gyrus	brain
13	chr3:19480000-19480400	Strong transcription	Fetal Brain Female	brain

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