Variant report

Variant	rs16986294
Chromosome Location	chr19:55682977-55682978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr19:55682718-55682997	K562	blood:	n/a	n/a
2	EP300	chr19:55682841-55683003	K562	blood:	n/a	n/a
3	TAL1	chr19:55682852-55683052	K562	blood:	n/a	n/a
4	IRF1	chr19:55682720-55683082	K562	blood:	n/a	n/a
5	RCOR1	chr19:55682845-55683081	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55682890..55686413-chr19:55726859..55729575,3	K562	blood:
2	chr19:55682815..55684434-chr19:55902687..55904944,2	K562	blood:
3	chr19:55220816..55222666-chr19:55680754..55683589,2	K562	blood:
4	chr19:55682875..55687636-chr19:55687850..55692874,6	MCF-7	breast:

No data

Variant related genes	Relation type
DNAAF3	TF binding region
ENSG00000267649	Chromatin interaction
ENSG00000129990	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10424609	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10424638	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669300	0.88[ASN][1000 genomes]
rs11670538	0.96[ASN][1000 genomes]
rs11672000	0.88[ASN][1000 genomes]
rs11672834	0.88[ASN][1000 genomes]
rs13343638	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16986289	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16986292	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729837	1.00[ASN][1000 genomes]
rs3729841	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs3859540	1.00[CEU][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3859542	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509927	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509930	1.00[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7248799	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8107129	0.96[ASN][1000 genomes]
rs8107736	0.96[ASN][1000 genomes]
rs8110415	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9749340	0.96[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	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16986294	ZNF552	cis	parietal	SCAN
rs16986294	ZNF324	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55679000-55684000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:55679400-55683800	Weak transcription	HMEC	breast
3	chr19:55679400-55684000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr19:55679400-55684000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr19:55679400-55684000	Weak transcription	Hela-S3	cervix
6	chr19:55679400-55684000	Weak transcription	NHEK	skin
7	chr19:55682800-55684400	Enhancers	K562	blood

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