Variant report

Variant	rs4885948
Chromosome Location	chr13:53309433-53309434
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	chr13:53305786..53308758-chr13:53309005..53310904,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11148262	1.00[JPT][hapmap]
rs1436724	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1436728	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1925135	1.00[JPT][hapmap]
rs2118093	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2760780	1.00[JPT][hapmap]
rs342774	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs342777	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3931491	1.00[JPT][hapmap]
rs4539485	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4542538	1.00[JPT][hapmap]
rs4884223	1.00[JPT][hapmap]
rs4885804	1.00[JPT][hapmap]
rs4885887	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4885910	1.00[JPT][hapmap]
rs617660	1.00[JPT][hapmap]
rs61961162	0.81[AMR][1000 genomes]
rs61961163	0.81[AMR][1000 genomes]
rs630892	1.00[JPT][hapmap]
rs646498	1.00[JPT][hapmap]
rs6561673	1.00[JPT][hapmap]
rs6561676	1.00[JPT][hapmap]
rs6561677	1.00[JPT][hapmap]
rs6561684	1.00[JPT][hapmap]
rs6561685	1.00[JPT][hapmap]
rs6561686	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs676306	1.00[JPT][hapmap]
rs693991	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7319451	1.00[CHD][hapmap]
rs7325840	1.00[JPT][hapmap]
rs7330193	1.00[JPT][hapmap]
rs7330361	1.00[JPT][hapmap]
rs7335270	1.00[JPT][hapmap]
rs7987405	1.00[JPT][hapmap]
rs7995188	1.00[JPT][hapmap]
rs7996692	1.00[JPT][hapmap]
rs7999466	1.00[JPT][hapmap]
rs8000715	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9316581	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9316583	1.00[JPT][hapmap]
rs9526957	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9526958	1.00[JPT][hapmap]
rs9526966	1.00[JPT][hapmap]
rs9526970	1.00[JPT][hapmap]
rs9526976	1.00[JPT][hapmap]
rs9526978	1.00[JPT][hapmap]
rs9526986	1.00[JPT][hapmap]
rs9526991	1.00[JPT][hapmap]
rs9526993	1.00[JPT][hapmap]
rs9526997	1.00[JPT][hapmap]
rs9536184	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9536222	1.00[JPT][hapmap]
rs9536228	1.00[JPT][hapmap]
rs9536232	1.00[JPT][hapmap]
rs9536238	1.00[JPT][hapmap]
rs9536241	1.00[JPT][hapmap]
rs9536244	1.00[JPT][hapmap]
rs9536245	1.00[JPT][hapmap]
rs9536248	1.00[JPT][hapmap]
rs9536249	1.00[JPT][hapmap]
rs9536250	1.00[JPT][hapmap]
rs9536257	1.00[JPT][hapmap]
rs9536259	1.00[JPT][hapmap]
rs9536260	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9568747	1.00[JPT][hapmap]
rs971513	1.00[JPT][hapmap]
rs973198	1.00[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1047265	chr13:53173013-53311419	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv541776	chr13:53173013-53311419	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4885948	CKAP2	cis	parietal	SCAN
rs4885948	CKAP2	cis	cerebellum	SCAN
rs4885948	ALG11	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53286800-53310800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:53298400-53310600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:53299000-53310400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:53303800-53311400	Weak transcription	Brain Anterior Caudate	brain
5	chr13:53306200-53310600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr13:53309000-53309600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr13:53309000-53309600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
8	chr13:53309000-53309600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
9	chr13:53309000-53309600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr13:53309000-53309600	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr13:53309000-53309600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr13:53309000-53309600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:53309200-53309800	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr13:53309400-53310600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr13:53309400-53312200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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