Variant report

Variant	rs463501
Chromosome Location	chr21:40016285-40016286
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40014305..40016339-chr21:40035627..40038289,2	MCF-7	breast:
2	chr21:40014328..40017749-chr21:40031360..40034967,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157554	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1015069	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1015070	1.00[CEU][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1540015	0.83[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1540016	1.00[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836613	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836619	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2836620	0.88[ASN][1000 genomes]
rs458783	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs459813	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs460112	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs460843	0.90[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs460947	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs461488	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs461592	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs463269	0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs463530	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs465004	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs465327	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62217514	0.89[EUR][1000 genomes]
rs6517476	0.88[ASN][1000 genomes]
rs8132920	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8134664	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9647180	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs994003	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9975531	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065541	chr21:40009959-40024976	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1057719	chr21:40009959-40025433	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1058663	chr21:40009959-40031681	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1055287	chr21:40013735-40031681	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs463501	SETD4	cis	parietal	SCAN
rs463501	RUNX1	cis	parietal	SCAN
rs463501	HLCS	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40012000-40016400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr21:40012800-40016800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr21:40014600-40016400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr21:40015600-40017400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr21:40016000-40017200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr21:40016000-40017400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr21:40016000-40018200	Weak transcription	Aorta	Aorta
8	chr21:40016000-40018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr21:40016000-40027000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:40016200-40017600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr21:40016200-40024000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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