Variant report

Variant	rs4523733
Chromosome Location	chr12:48927514-48927515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10747550	0.86[CHB][hapmap]
rs10783262	0.86[CHB][hapmap]
rs11168599	0.83[TSI][hapmap]
rs11168637	0.81[TSI][hapmap]
rs11458	0.83[TSI][hapmap]
rs12371700	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs12425460	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12815544	0.81[CEU][hapmap]
rs1895999	0.86[CHB][hapmap]
rs4076368	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4237859	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4409884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4492859	0.86[CHB][hapmap]
rs4760721	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760723	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301368	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974213	0.83[TSI][hapmap]
rs7974371	0.93[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.84[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	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1047600	chr12:48927514-48954225	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1048307	chr12:48927514-48958949	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4523733	C12orf54	cis	cerebellum	SCAN
rs4523733	OR10AD1	cis	cerebellum	SCAN
rs4523733	RHEBL1	cis	cerebellum	SCAN
rs4523733	RPAP3	cis	cerebellum	SCAN
rs4523733	CCNT1	cis	cerebellum	SCAN
rs4523733	C12orf54	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48924400-48927800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr12:48924600-48927800	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr12:48925200-48927800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr12:48925200-48928000	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr12:48926000-48927600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr12:48926600-48927800	Enhancers	Primary T cells from cord blood	blood
7	chr12:48927000-48927600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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

what's new

Quick links