Variant report

Variant	rs290432
Chromosome Location	chr20:52676295-52676296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52556030..52560309-chr20:52671948..52677336,4	K562	blood:
2	chr20:52674058..52677861-chr20:52678021..52680977,4	K562	blood:
3	chr20:52675939..52678149-chr20:53262263..53264864,2	MCF-7	breast:
4	chr17:59488569..59490158-chr20:52676107..52678270,2	MCF-7	breast:
5	chr20:52561689..52563690-chr20:52674692..52676871,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267280	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000236352	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs103926	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs290392	0.81[CHD][hapmap]
rs290430	0.94[ASN][1000 genomes]
rs290431	0.91[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs290436	0.86[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290441	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs290444	0.81[JPT][hapmap]
rs290445	0.82[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs290446	0.88[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs290448	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs290449	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs458674	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs459113	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs460317	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs460470	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs462174	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs463420	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs463722	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs467267	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs467321	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs756021	0.84[CEU][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs290432	BCAS1	cis	multi-tissue	Pritchard
rs290432	BCAS1	cis	Lymphoblastoid	GTEx
rs290432	BCAS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
2	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr20:52669400-52681800	Weak transcription	Gastric	stomach
4	chr20:52674400-52681200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr20:52674400-52682000	Weak transcription	Colonic Mucosa	Colon
6	chr20:52674800-52677600	Weak transcription	NHDF-Ad	bronchial
7	chr20:52675000-52677400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr20:52675000-52683000	Weak transcription	HepG2	liver
9	chr20:52675200-52678800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr20:52675400-52679200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr20:52675600-52679200	Weak transcription	K562	blood
12	chr20:52675600-52679600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr20:52675800-52679600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr20:52676200-52676800	ZNF genes & repeats	GM12878-XiMat	blood

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