Variant report

Variant	rs2150409
Chromosome Location	chr21:40251190-40251191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	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

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs13050863	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1475592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1785432	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2210265	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836722	0.84[CEU][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap]
rs2836723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836726	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836742	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs455152	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461737	0.82[ASN][1000 genomes]
rs463442	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs464093	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467788	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs468042	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs468637	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs469031	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs469043	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs469368	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4816606	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4816607	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6517485	0.87[ASN][1000 genomes]
rs8133009	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9653664	0.84[CEU][hapmap]
rs992242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992243	0.83[CEU][hapmap]
rs992244	0.84[CEU][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2150409	FAM19A4	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40247800-40259400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:40249800-40251600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr21:40250000-40251200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr21:40250400-40252400	Enhancers	Liver	Liver
5	chr21:40251000-40251600	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links