Variant report

Variant	rs2836722
Chromosome Location	chr21:40250008-40250009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40241705..40244760-chr21:40247140..40250390,3	K562	blood:
2	chr21:40031187..40034113-chr21:40248708..40250685,2	MCF-7	breast:
3	chr21:40249695..40251882-chr21:40278200..40280440,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSMG1-9	chr21:40249215-40252276	ENSG00000205622
2	lnc-PSMG1-9	chr21:40249215-40252296	ENSG00000205622

Variant related genes	Relation type
ENSG00000157554	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10854390	0.82[ASN][1000 genomes]
rs12481753	0.81[ASN][1000 genomes]
rs12482288	0.82[ASN][1000 genomes]
rs12483491	0.82[ASN][1000 genomes]
rs13048952	0.82[ASN][1000 genomes]
rs13050477	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs13051097	0.82[ASN][1000 genomes]
rs1475592	0.83[CEU][hapmap]
rs2032171	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032172	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094873	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs2150409	0.84[CEU][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap]
rs2210265	0.82[MEX][hapmap]
rs2836718	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2836719	0.82[ASN][1000 genomes]
rs2836723	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs2836725	0.83[CEU][hapmap]
rs2836735	0.81[CHB][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs2836737	0.86[GIH][hapmap]
rs2836740	0.81[ASN][1000 genomes]
rs4143382	0.99[ASN][1000 genomes]
rs4432550	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467788	0.81[EUR][1000 genomes]
rs468042	0.81[EUR][1000 genomes]
rs469043	0.81[EUR][1000 genomes]
rs469368	0.81[EUR][1000 genomes]
rs469443	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469524	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4817966	0.82[ASN][1000 genomes]
rs7275685	0.82[ASN][1000 genomes]
rs7276441	0.82[ASN][1000 genomes]
rs7277330	0.82[ASN][1000 genomes]
rs7279223	0.82[ASN][1000 genomes]
rs7279660	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8126904	0.81[ASN][1000 genomes]
rs8131220	0.82[ASN][1000 genomes]
rs9653664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9680142	0.82[ASN][1000 genomes]
rs9680143	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs992242	0.84[CEU][hapmap];0.86[MEX][hapmap]
rs992243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[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];0.97[EUR][1000 genomes];1.00[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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv587478	chr21:40243459-40275033	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2836722	PCP4	cis	cerebellum	SCAN
rs2836722	FAM19A4	trans	cerebellum	SCAN
rs2836722	TUBB2C	trans	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40247800-40250200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr21:40247800-40250400	Weak transcription	HMEC	breast
3	chr21:40247800-40259400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr21:40248600-40250600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr21:40249800-40251600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr21:40250000-40250600	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr21:40250000-40251200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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