Variant report

Variant	rs527987
Chromosome Location	chr21:40921020-40921021
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40919721..40922141-chr21:40925056..40927590,2	MCF-7	breast:
2	chr21:40918819..40921569-chr21:40925046..40926881,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11088484	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs12626648	0.84[ASN][1000 genomes]
rs12626661	0.89[ASN][1000 genomes]
rs2837075	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2837076	0.80[CEU][hapmap]
rs28644269	0.94[ASN][1000 genomes]
rs4372991	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474852	0.83[AFR][1000 genomes]
rs477483	0.80[CEU][hapmap]
rs479578	0.83[AFR][1000 genomes]
rs480386	0.85[AFR][1000 genomes]
rs4818051	0.84[ASN][1000 genomes]
rs482389	0.82[AFR][1000 genomes]
rs485757	0.81[ASW][hapmap];0.80[CEU][hapmap]
rs490214	0.85[AFR][1000 genomes]
rs494815	0.85[AFR][1000 genomes]
rs516888	0.88[ASN][1000 genomes]
rs517871	0.88[ASN][1000 genomes]
rs521559	0.88[ASN][1000 genomes]
rs551558	0.85[AFR][1000 genomes]
rs551699	0.85[AFR][1000 genomes]
rs560554	0.83[AFR][1000 genomes]
rs561340	0.87[ASW][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs56178310	0.84[ASN][1000 genomes]
rs574863	0.89[ASN][1000 genomes]
rs587935	0.88[ASN][1000 genomes]
rs588903	0.89[ASN][1000 genomes]
rs591457	0.81[ASW][hapmap];0.80[CEU][hapmap]
rs592738	0.85[AFR][1000 genomes]
rs594005	0.85[AFR][1000 genomes]
rs608265	0.85[AFR][1000 genomes]
rs619766	0.89[ASN][1000 genomes]
rs622712	0.83[AFR][1000 genomes]
rs623605	0.83[AFR][1000 genomes]
rs623994	0.83[AFR][1000 genomes]
rs624037	0.82[AFR][1000 genomes]
rs624436	0.83[AFR][1000 genomes]
rs624900	0.83[AFR][1000 genomes]
rs625760	0.83[AFR][1000 genomes]
rs626887	0.85[AFR][1000 genomes]
rs633208	0.81[JPT][hapmap]
rs636776	0.83[AFR][1000 genomes]
rs656582	0.86[ASN][1000 genomes]
rs656618	0.92[ASN][1000 genomes]
rs670316	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680944	0.88[ASN][1000 genomes]
rs681447	0.88[ASN][1000 genomes]
rs685238	0.85[AFR][1000 genomes]
rs685732	0.83[AFR][1000 genomes]
rs686185	0.83[AFR][1000 genomes]
rs686540	0.85[AFR][1000 genomes]
rs686542	0.85[AFR][1000 genomes]
rs687031	0.85[AFR][1000 genomes]
rs687537	0.81[AFR][1000 genomes]
rs687940	0.85[AFR][1000 genomes]
rs689362	0.85[AFR][1000 genomes]
rs73356097	0.91[AFR][1000 genomes]
rs7410119	0.93[ASN][1000 genomes]
rs8127424	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8128108	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8130455	0.84[ASN][1000 genomes]
rs9984946	0.85[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs527987	GNA13	trans	parietal	SCAN
rs527987	DOPEY2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40914600-40923600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr21:40921000-40925000	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links