Variant report

Variant	rs456325
Chromosome Location	chr16:12012562-12012563
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12010326..12012796-chr16:12069017..12071833,3	MCF-7	breast:
2	chr16:12012124..12014555-chr16:12045355..12047902,2	K562	blood:
3	chr16:12010494..12013016-chr16:12016316..12019639,3	MCF-7	breast:
4	chr16:12010691..12013114-chr16:12155698..12158691,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234719	Chromatin interaction
ENSG00000048471	Chromatin interaction
ENSG00000260488	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs190461	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2018199	1.00[CEU][hapmap]
rs2075158	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs256400	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs33619	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs33620	0.82[EUR][1000 genomes]
rs33621	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33623	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs33624	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33629	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33630	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33631	0.85[CEU][hapmap]
rs33635	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33638	0.84[ASN][1000 genomes]
rs33648	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs33654	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33655	0.85[CEU][hapmap]
rs33660	0.88[CEU][hapmap]
rs40311	0.88[CEU][hapmap]
rs42424	0.87[EUR][1000 genomes]
rs4429311	0.81[JPT][hapmap]
rs4493057	0.83[CEU][hapmap];0.80[JPT][hapmap]
rs4511557	0.84[CEU][hapmap]
rs7198817	0.80[CEU][hapmap]
rs7202234	0.88[CEU][hapmap]
rs8061189	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1735	chr16:11986963-12031597	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv974848	chr16:12005053-12020022	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
5	nsv524025	chr16:12009781-12016919	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
6	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	esv3379697	chr16:12011449-12049700	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs456325	GSPT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12011600-12014600	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links