Variant report

Variant	rs555963
Chromosome Location	chr21:40948546-40948547
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	chr21:40936564..40938095-chr21:40947433..40949927,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11701943	0.81[YRI][hapmap]
rs12627708	1.00[JPT][hapmap]
rs1734930	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2837074	0.90[ASN][1000 genomes]
rs2837083	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2989335	0.90[ASN][1000 genomes]
rs492140	1.00[ASN][1000 genomes]
rs503729	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs506387	1.00[ASN][1000 genomes]
rs516865	1.00[ASN][1000 genomes]
rs523372	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs526526	1.00[ASN][1000 genomes]
rs527343	1.00[ASN][1000 genomes]
rs528499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs535457	0.92[CEU][hapmap]
rs536444	0.92[CEU][hapmap]
rs538333	1.00[ASN][1000 genomes]
rs542531	1.00[ASN][1000 genomes]
rs551439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs551624	1.00[ASN][1000 genomes]
rs551680	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs551830	1.00[ASN][1000 genomes]
rs554401	0.91[CEU][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]
rs561166	1.00[ASN][1000 genomes]
rs562285	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs563230	1.00[ASN][1000 genomes]
rs563259	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs564126	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs567837	1.00[ASN][1000 genomes]
rs568840	0.90[ASN][1000 genomes]
rs571227	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs579841	0.90[ASN][1000 genomes]
rs585092	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs59155174	1.00[ASN][1000 genomes]
rs596320	1.00[ASN][1000 genomes]
rs602107	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs606003	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs606414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs611039	1.00[ASN][1000 genomes]
rs611958	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs613758	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs617259	1.00[ASN][1000 genomes]
rs626856	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs628995	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs629432	1.00[ASN][1000 genomes]
rs630270	1.00[ASN][1000 genomes]
rs631454	1.00[ASN][1000 genomes]
rs636599	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs644080	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs646823	1.00[ASN][1000 genomes]
rs647448	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs650633	1.00[ASN][1000 genomes]
rs651607	1.00[ASN][1000 genomes]
rs657833	0.90[ASN][1000 genomes]
rs658066	1.00[ASN][1000 genomes]
rs665778	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	33 gene(s)	inside rSNPs	diseases
3	esv2756754	chr21:40857523-40966156	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2758820	chr21:40857523-40966156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv34779	chr21:40884871-40977473	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv433457	chr21:40900348-40964553	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1057956	chr21:40907707-41393396	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv544444	chr21:40907707-41393396	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	esv17842	chr21:40918970-40965975	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs555963	DOPEY2	cis	cerebellum	SCAN
rs555963	BRWD1	cis	parietal	SCAN
rs555963	LPAR6	trans	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40947400-40949000	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr21:40947600-40949200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr21:40948000-40948600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr21:40948200-40948800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr21:40948200-40948800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr21:40948200-40949400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr21:40948400-40948800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr21:40948400-40948800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr21:40948400-40948800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:40948400-40948800	Enhancers	H9 Cell Line	embryonic stem cell
11	chr21:40948400-40948800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr21:40948400-40948800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr21:40948400-40948800	Enhancers	Fetal Heart	heart
14	chr21:40948400-40948800	Enhancers	Placenta	Placenta
15	chr21:40948400-40948800	Enhancers	Left Ventricle	heart
16	chr21:40948400-40949000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr21:40948400-40949000	Enhancers	Stomach Mucosa	stomach

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