Variant report

Variant	rs12807017
Chromosome Location	chr11:9679145-9679146
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr11:9679138-9679484	GM12878	blood:	n/a	n/a
2	BHLHE40	chr11:9679093-9679293	HepG2	liver:	n/a	n/a
3	BHLHE40	chr11:9679032-9679391	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000239470	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10770044	0.86[CEU][hapmap]
rs10770051	0.93[EUR][1000 genomes]
rs10840283	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840284	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840286	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840287	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11042437	0.81[CEU][hapmap]
rs11042439	0.95[CEU][hapmap];0.86[GIH][hapmap]
rs11042440	0.95[CEU][hapmap];0.86[GIH][hapmap]
rs11042441	0.95[CEU][hapmap];0.86[GIH][hapmap]
rs11042457	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042462	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042464	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042466	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042467	1.00[ASN][1000 genomes]
rs11042486	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11042500	1.00[CHB][hapmap]
rs11042511	1.00[CHB][hapmap]
rs11600183	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11601008	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603527	1.00[ASN][1000 genomes]
rs11607321	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607776	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11607900	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362879	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364089	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421878	1.00[CHB][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs12422111	0.81[GIH][hapmap]
rs12786236	1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs12789209	1.00[ASN][1000 genomes]
rs12789429	1.00[ASN][1000 genomes]
rs12794270	1.00[ASN][1000 genomes]
rs12797744	1.00[ASN][1000 genomes]
rs12801958	1.00[ASN][1000 genomes]
rs12803440	1.00[ASN][1000 genomes]
rs12805683	1.00[ASN][1000 genomes]
rs12808226	1.00[CHB][hapmap]
rs17268632	1.00[CHB][hapmap]
rs34063054	1.00[ASN][1000 genomes]
rs35806232	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089180	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910060	1.00[ASN][1000 genomes]
rs4910486	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910487	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910488	1.00[ASN][1000 genomes]
rs4910492	1.00[ASN][1000 genomes]
rs4910493	1.00[ASN][1000 genomes]
rs4910497	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4910505	1.00[CHB][hapmap]
rs56043731	1.00[ASN][1000 genomes]
rs67867011	1.00[ASN][1000 genomes]
rs7120616	0.95[CEU][hapmap]
rs72852112	1.00[ASN][1000 genomes]
rs7943610	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896986	chr11:9636854-9679145	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv972945	chr11:9660423-9684250	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv971987	chr11:9674511-9684250	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12807017	ASCL3	cis	parietal	SCAN
rs12807017	OR2D2	cis	cerebellum	SCAN
rs12807017	RIC3	cis	cerebellum	SCAN
rs12807017	LCORL	trans	parietal	SCAN
rs12807017	TMEM41B	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9674000-9684000	Weak transcription	HSMMtube	muscle
2	chr11:9674000-9684800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:9674200-9684800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr11:9678400-9682200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:9678400-9684000	Weak transcription	Placenta	Placenta
6	chr11:9678400-9684200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr11:9678800-9679200	Enhancers	GM12878-XiMat	blood
8	chr11:9678800-9680400	Enhancers	HepG2	liver
9	chr11:9679000-9679200	Enhancers	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links