Variant report

Variant	rs6925255
Chromosome Location	chr6:80466124-80466125
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	chr6:80465546..80468077-chr6:80483987..80486479,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12212008	0.92[EUR][1000 genomes]
rs12660740	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2207369	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2223978	0.83[ASN][1000 genomes]
rs2322449	0.82[ASN][1000 genomes]
rs2322450	0.81[ASN][1000 genomes]
rs2322451	0.81[ASN][1000 genomes]
rs2874794	0.83[ASN][1000 genomes]
rs4467741	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4706101	0.85[EUR][1000 genomes]
rs59337495	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6900699	0.85[EUR][1000 genomes]
rs6921089	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6941826	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs714701	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs714702	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs714703	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs714704	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs720808	0.82[AMR][1000 genomes]
rs761605	0.98[EUR][1000 genomes]
rs7768071	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs926839	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9350827	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9352763	0.83[ASN][1000 genomes]
rs9352765	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9361558	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9443716	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9448820	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1021143	chr6:80400195-80598163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv886305	chr6:80433732-80495689	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv12341	chr6:80461435-80476237	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Aging	22773346	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6925255	HMGN3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80464800-80466800	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links