Variant report

Variant	rs12144635
Chromosome Location	chr1:173246262-173246263
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	YY1	chr1:173246117-173246352	K562	blood:	n/a	n/a
2	YY1	chr1:173245865-173246365	GM12878	blood:	n/a	chr1:173245989-173245997 chr1:173245978-173246000
3	USF1	chr1:173246161-173246367	GM12878	blood:	n/a	n/a
4	BHLHE40	chr1:173246042-173246454	GM12878	blood:	n/a	n/a
5	TCF3	chr1:173246129-173246354	GM12878	blood:	n/a	n/a
6	EBF1	chr1:173246134-173246441	GM12878	blood:	n/a	n/a
7	TCF3	chr1:173246147-173246440	GM12878	blood:	n/a	n/a
8	PAX5	chr1:173246104-173246363	GM12878	blood:	n/a	n/a
9	MAX	chr1:173246200-173246314	NB4	blood:	n/a	chr1:173246279-173246286 chr1:173246277-173246287 chr1:173246276-173246289 chr1:173246278-173246288 chr1:173246277-173246288 chr1:173246278-173246287 chr1:173246279-173246288 chr1:173246274-173246289 chr1:173246278-173246287 chr1:173246276-173246289
10	USF1	chr1:173246202-173246350	GM12878	blood:	n/a	n/a
11	IKZF1	chr1:173246074-173246434	GM12878	blood:	n/a	n/a
12	NFIC	chr1:173245868-173246638	GM12878	blood:	n/a	n/a
13	RUNX3	chr1:173246036-173246487	GM12878	blood:	n/a	n/a
14	RUNX3	chr1:173246006-173246462	GM12878	blood:	n/a	n/a
15	TBL1XR1	chr1:173246090-173246608	GM12878	blood:	n/a	n/a
16	ATF2	chr1:173245948-173246479	GM12878	blood:	n/a	n/a
17	BCLAF1	chr1:173246026-173246619	GM12878	blood:	n/a	chr1:173246062-173246071 chr1:173246082-173246091
18	POLR2A	chr1:173246046-173250055	K562	blood:	n/a	n/a
19	MTA3	chr1:173245942-173246573	GM12878	blood:	n/a	n/a
20	BATF	chr1:173246073-173246494	GM12878	blood:	n/a	n/a
21	EP300	chr1:173246058-173246372	GM12878	blood:	n/a	n/a
22	BATF	chr1:173246058-173246468	GM12878	blood:	n/a	n/a
23	YY1	chr1:173245804-173246334	GM12878	blood:	n/a	chr1:173245989-173245997 chr1:173245978-173246000
24	TCF12	chr1:173246032-173246366	GM12878	blood:	n/a	chr1:173246186-173246193
25	USF2	chr1:173246122-173246471	GM12878	blood:	n/a	n/a
26	NFIC	chr1:173245961-173246541	GM12878	blood:	n/a	n/a
27	PAX5	chr1:173246038-173246519	GM12878	blood:	n/a	chr1:173246082-173246091
28	EBF1	chr1:173246071-173246385	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000251817	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10465507	0.82[ASN][1000 genomes]
rs10489266	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs10489268	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs10798264	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs10912558	0.82[ASN][1000 genomes]
rs10912560	1.00[CHB][hapmap]
rs10912561	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs11587348	0.82[ASN][1000 genomes]
rs11801818	0.82[ASN][1000 genomes]
rs11806687	0.82[ASN][1000 genomes]
rs11807031	0.82[ASN][1000 genomes]
rs11808060	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12119090	0.91[ASN][1000 genomes]
rs12120808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125395	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138547	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141186	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13343108	1.00[CHB][hapmap]
rs17300347	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs17300677	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17300754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17346501	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs17372309	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4090392	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs4113832	0.82[ASN][1000 genomes]
rs4916210	0.82[ASN][1000 genomes]
rs4916314	0.82[ASN][1000 genomes]
rs56074681	0.82[ASN][1000 genomes]
rs57928823	0.82[ASN][1000 genomes]
rs61826345	0.82[ASN][1000 genomes]
rs61828261	0.82[ASN][1000 genomes]
rs61828267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72722845	0.82[ASN][1000 genomes]
rs72722865	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12144635	UBXN1	trans	cerebellum	SCAN
rs12144635	TNFSF18	cis	cerebellum	SCAN
rs12144635	UBAP2	trans	cerebellum	SCAN
rs12144635	TNFSF4	cis	cerebellum	SCAN
rs12144635	KLHL20	cis	parietal	SCAN
rs12144635	F5	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173244800-173248600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr1:173245000-173247800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:173245000-173247800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:173245400-173247000	Enhancers	GM12878-XiMat	blood
5	chr1:173246000-173246400	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links