Variant report

Variant	rs12082659
Chromosome Location	chr1:93292347-93292348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93290582..93295028-chr1:93295962..93297870,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122406	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10874745	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164825	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11582791	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586089	1.00[ASN][1000 genomes]
rs11586570	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062315	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12726286	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728322	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746956	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750269	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1854797	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2893226	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34041593	0.86[ASN][1000 genomes]
rs34098754	0.86[ASN][1000 genomes]
rs34168045	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34244251	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031391	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35051335	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183060	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270016	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604026	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66525381	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657809	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687931	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71652510	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514280	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521417	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554594	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv530047	chr1:93273425-93308213	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv508393	chr1:93290513-93344924	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv511706	chr1:93291077-93294396	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3452383	chr1:93291564-93293256	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3452384	chr1:93291943-93292882	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3452385	chr1:93291943-93292882	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12082659	FAM69A	cis	Artery Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93289800-93292400	Weak transcription	HepG2	liver
2	chr1:93289800-93297400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:93292200-93292600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links