Variant report

Variant	rs7279660
Chromosome Location	chr21:40236810-40236811
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	chr21:40176800..40178913-chr21:40235378..40237558,2	K562	blood:
2	chr21:40225467..40227132-chr21:40235439..40238376,2	K562	blood:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10854390	0.82[ASN][1000 genomes]
rs12481753	0.80[ASN][1000 genomes]
rs12482288	0.82[ASN][1000 genomes]
rs12483491	0.82[ASN][1000 genomes]
rs13048952	0.82[ASN][1000 genomes]
rs13050477	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs13051097	0.82[ASN][1000 genomes]
rs2032171	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2032172	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2094873	0.86[CHB][hapmap]
rs2836718	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];0.82[ASN][1000 genomes]
rs2836719	0.82[ASN][1000 genomes]
rs2836722	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]
rs2836735	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs2836740	0.80[ASN][1000 genomes]
rs4143382	0.98[ASN][1000 genomes]
rs4432550	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs469443	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs469524	0.83[AMR][1000 genomes];0.99[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]
rs8126904	0.80[ASN][1000 genomes]
rs8131220	0.82[ASN][1000 genomes]
rs9653664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9680142	0.82[ASN][1000 genomes]
rs9680143	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs992243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs992244	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]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7279660	PCP4	cis	cerebellum	SCAN
rs7279660	CHAF1B	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40226000-40242200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr21:40229600-40245400	Weak transcription	Left Ventricle	heart
3	chr21:40232400-40237200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr21:40233600-40245400	Weak transcription	Right Atrium	heart
5	chr21:40235600-40247600	Weak transcription	Spleen	Spleen
6	chr21:40236800-40237600	Enhancers	H1 Cell Line	embryonic stem cell

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