Variant report

Variant	rs5997960
Chromosome Location	chr22:31747786-31747787
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	chr22:31746827..31749730-chr22:31771450..31774509,3	MCF-7	breast:
2	chr17:61043432..61045215-chr22:31745449..31748247,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263931	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11703927	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12166373	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12167361	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13053245	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13056815	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13057841	0.80[EUR][1000 genomes]
rs13058363	0.81[EUR][1000 genomes]
rs131200	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131202	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131209	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131213	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131219	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs140074	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs140077	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2009132	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2013254	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413048	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28523714	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28715	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28813120	0.90[EUR][1000 genomes]
rs34873968	0.80[EUR][1000 genomes]
rs4820045	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4820961	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820969	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753558	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5753576	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5994397	0.81[EUR][1000 genomes]
rs5997909	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997919	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5997929	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997932	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997938	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997971	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5997980	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs5997981	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs713947	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7285171	0.89[EUR][1000 genomes]
rs7287402	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7288643	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7288735	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7289189	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7289337	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs739427	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8141987	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8143002	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs926928	0.82[EUR][1000 genomes]
rs9606835	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9609263	0.84[AMR][1000 genomes]
rs9619187	0.94[EUR][1000 genomes]
rs9621216	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9621221	0.90[EUR][1000 genomes]
rs9621227	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	esv3333136	chr22:31704947-31758417	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv1816779	chr22:31743711-31797094	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5997960	SFI1	cis	Thyroid	GTEx
rs5997960	DRG1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31744000-31762200	Weak transcription	Right Atrium	heart
2	chr22:31744200-31748400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr22:31744200-31750400	Weak transcription	Spleen	Spleen
4	chr22:31745200-31751400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:31747000-31748200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr22:31747000-31750400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr22:31747400-31747800	Weak transcription	HepG2	liver

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