Variant report

Variant	rs6800897
Chromosome Location	chr3:68066484-68066485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:67840426..67841246-chr3:68065943..68066794,2	MCF-7	breast:
2	chr3:67951890..67952870-chr3:68066397..68066948,2	MCF-7	breast:
3	chr3:67160040..67160708-chr3:68065971..68066562,2	MCF-7	breast:
4	chr3:67869894..67870930-chr3:68066062..68066983,4	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12497186	0.83[CEU][hapmap]
rs13100924	0.83[CEU][hapmap]
rs1349005	0.82[GIH][hapmap]
rs1374837	0.94[ASW][hapmap];0.87[CEU][hapmap];0.93[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap]
rs35033704	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35471768	0.95[ASN][1000 genomes]
rs6792729	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6793147	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796173	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs7373042	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs7429717	0.86[GIH][hapmap];0.93[MEX][hapmap]
rs7430276	0.82[CEU][hapmap]
rs7431117	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs7625708	0.83[CEU][hapmap]
rs7632136	0.82[CEU][hapmap]
rs9812127	0.87[CEU][hapmap]
rs9818541	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs9857691	0.82[GIH][hapmap]
rs9869498	0.83[CEU][hapmap];0.84[JPT][hapmap]
rs9874728	0.82[CEU][hapmap];0.89[GIH][hapmap];0.81[MEX][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	nsv1002010	chr3:67785913-68312064	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1009871	chr3:67862617-68312064	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv536583	chr3:67862617-68312064	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1010231	chr3:67894825-68117879	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1013531	chr3:67917771-68070027	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv999747	chr3:68066423-68188180	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv536584	chr3:68066423-68188180	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6800897	LRIG1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links