Variant report

Variant	rs4884522
Chromosome Location	chr13:53053768-53053769
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53049275..53051586-chr13:53052175..53054640,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1057478	0.90[ASW][hapmap];0.80[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap]
rs11148252	0.91[ASW][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap]
rs11616459	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11618716	0.81[ASW][hapmap];0.89[LWK][hapmap];0.95[MKK][hapmap]
rs1924036	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs2575960	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap]
rs2760815	0.88[CEU][hapmap]
rs3886077	0.81[ASW][hapmap];0.91[LWK][hapmap]
rs4286007	0.81[ASW][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap]
rs4301905	0.81[ASN][1000 genomes]
rs4335671	0.81[ASN][1000 genomes]
rs4884452	0.91[ASW][hapmap];0.91[LWK][hapmap]
rs4886018	0.91[ASW][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap]
rs55688428	0.89[ASN][1000 genomes]
rs61959716	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7328729	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs7334137	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs7334677	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs7336771	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs7987115	0.91[ASW][hapmap];0.92[LWK][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap]
rs7990581	0.81[ASW][hapmap];0.89[MKK][hapmap]
rs7993748	0.81[ASW][hapmap]
rs9526913	0.81[ASW][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap]
rs9526929	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526968	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs9526974	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap]
rs9536066	0.81[ASW][hapmap];0.82[MKK][hapmap]
rs9536079	0.89[MKK][hapmap]
rs9536104	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap]
rs9536211	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs9536212	0.92[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap]
rs9536219	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap]
rs9536220	0.83[CHB][hapmap];0.81[YRI][hapmap]
rs9563113	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs9563114	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs9568732	0.81[ASW][hapmap];0.82[MKK][hapmap]
rs9568734	0.81[ASW][hapmap];0.82[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv900085	chr13:53022518-53216622	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv900086	chr13:53030565-53208030	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv976117	chr13:53051476-53058376	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2421964	chr13:53051526-53160234	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4884522	SUGT1	cis	cerebellum	SCAN
rs4884522	HNRNPA1L2	cis	parietal	SCAN
rs4884522	CKAP2	cis	cerebellum	SCAN
rs4884522	CKAP2	cis	Artery Tibial	GTEx
rs4884522	CKAP2	cis	parietal	SCAN
rs4884522	HNRNPA1L2	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53030200-53053800	Weak transcription	Small Intestine	intestine
2	chr13:53030400-53055800	Weak transcription	Lung	lung
3	chr13:53034400-53054400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr13:53038200-53055400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr13:53042800-53054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:53049400-53054000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr13:53049600-53054000	Weak transcription	Liver	Liver
8	chr13:53050000-53055400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:53050000-53058800	Weak transcription	HepG2	liver
10	chr13:53051000-53055400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr13:53051400-53054800	Weak transcription	Osteobl	bone
12	chr13:53051400-53055200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:53051400-53055400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr13:53051400-53055400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr13:53051800-53055000	Weak transcription	HMEC	breast
16	chr13:53052000-53055200	Weak transcription	HSMM	muscle
17	chr13:53052200-53053800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:53052200-53053800	Weak transcription	Monocytes-CD14+_RO01746	blood

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