Variant report

Variant	rs2823131
Chromosome Location	chr21:16567728-16567729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:16258372..16261143-chr21:16567460..16569411,2	MCF-7	breast:
2	chr21:16235732..16237264-chr21:16566458..16569331,2	MCF-7	breast:
3	chr21:16492732..16495693-chr21:16564937..16568393,3	MCF-7	breast:
4	chr21:16429926..16439498-chr21:16561851..16585948,113	MCF-7	breast:
5	chr21:16421751..16443998-chr21:16557859..16589610,273	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180530	Chromatin interaction
ENSG00000236471	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11088317	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11909473	0.84[ASN][1000 genomes]
rs2205439	1.00[JPT][hapmap]
rs2403907	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2823125	1.00[JPT][hapmap]
rs2823128	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823129	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823133	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823134	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2823135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2823136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2823137	0.85[CEU][hapmap];0.80[CHB][hapmap];0.85[GIH][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes]
rs2823138	0.93[ASW][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs2823139	0.86[ASW][hapmap];0.81[LWK][hapmap]
rs60893125	0.88[AFR][1000 genomes]
rs7275438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275695	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7276622	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7282349	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926167	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063385	chr21:16521617-16926212	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv913413	chr21:16537728-16621859	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv33078	chr21:16566497-16567729	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2823131	TSSC4	trans	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16556600-16568000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:16564800-16567800	Weak transcription	Fetal Intestine Large	intestine
3	chr21:16564800-16569400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr21:16564800-16569400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr21:16565000-16571000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr21:16565800-16573400	Enhancers	HepG2	liver
7	chr21:16566800-16571800	Weak transcription	K562	blood
8	chr21:16567200-16568400	Enhancers	Liver	Liver
9	chr21:16567600-16568800	Enhancers	Fetal Intestine Small	intestine

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