Variant report

Variant	rs4412789
Chromosome Location	chr12:60242468-60242469
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	chr12:60240866..60243089-chr12:60312800..60315129,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10784007	0.85[AMR][1000 genomes]
rs10877352	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173169	0.83[ASN][1000 genomes]
rs11173170	0.87[ASN][1000 genomes]
rs11173171	0.87[ASN][1000 genomes]
rs11173189	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173197	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173199	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173200	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173201	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11173202	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049943	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230605	0.87[AMR][1000 genomes]
rs12298637	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2365314	0.83[ASN][1000 genomes]
rs2365315	0.83[ASN][1000 genomes]
rs4387384	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4417320	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4539371	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4623939	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758741	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4758846	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56098460	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7296099	0.85[AMR][1000 genomes]
rs7299153	0.82[AMR][1000 genomes]
rs7975905	0.83[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	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899134	chr12:60141518-60263723	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4412789	AVIL	cis	parietal	SCAN
rs4412789	AVIL	cis	cerebellum	SCAN
rs4412789	GPR84	cis	cerebellum	SCAN
rs4412789	KIF5A	cis	cerebellum	SCAN
rs4412789	DTX3	cis	cerebellum	SCAN
rs4412789	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL
rs4412789	NCKAP1L	cis	cerebellum	SCAN
rs4412789	OR6C6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60239200-60243800	Weak transcription	HUVEC	blood vessel
2	chr12:60240600-60243000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:60242200-60295600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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