Variant report

Variant	rs11793753
Chromosome Location	chr9:117460150-117460151
allele	A/G
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	IRF4	chr9:117460120-117460693	GM12878	blood:	n/a	n/a
2	CHD1	chr9:117460094-117460283	GM12878	blood:	n/a	n/a
3	RUNX3	chr9:117460051-117460795	GM12878	blood:	n/a	n/a
4	POU2F2	chr9:117460128-117460634	GM12891	blood:	n/a	n/a
5	RCOR1	chr9:117459520-117460265	IMR90	lung:	n/a	n/a
6	NFIC	chr9:117460126-117460861	GM12878	blood:	n/a	n/a
7	MTA3	chr9:117458874-117460796	GM12878	blood:	n/a	n/a
8	ATF2	chr9:117460149-117460803	GM12878	blood:	n/a	n/a
9	TBL1XR1	chr9:117458990-117460733	GM12878	blood:	n/a	n/a
10	BATF	chr9:117460081-117460757	GM12878	blood:	n/a	chr9:117460429-117460440
11	SMC3	chr9:117460133-117460294	GM12878	blood:	n/a	n/a
12	ESRRA	chr9:117458747-117461479	GM12878	blood:	n/a	chr9:117459306-117459322 chr9:117461416-117461426 chr9:117461414-117461427 chr9:117459301-117459317 chr9:117461414-117461430 chr9:117459308-117459318 chr9:117461414-117461426 chr9:117459308-117459318
13	RUNX3	chr9:117458835-117460867	GM12878	blood:	n/a	n/a
14	CEBPB	chr9:117460047-117460856	GM12878	blood:	n/a	n/a
15	JUND	chr9:117458957-117460721	GM12878	blood:	n/a	chr9:117459655-117459664 chr9:117459656-117459667 chr9:117459655-117459662 chr9:117459655-117459663 chr9:117459653-117459664 chr9:117459654-117459663
16	FOXM1	chr9:117458792-117460455	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000230284	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11788301	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11788303	1.00[ASN][1000 genomes]
rs11789254	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789913	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790078	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791529	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11793039	0.92[ASW][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11793592	1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11793719	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11794319	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11794322	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930795	0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16930798	0.81[LWK][hapmap]
rs16930910	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930928	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235713	1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17237046	0.84[AFR][1000 genomes]
rs17816047	0.84[ASW][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.82[AFR][1000 genomes]
rs2031877	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420964	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41278671	0.81[EUR][1000 genomes]
rs56357980	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
2	nsv831694	chr9:117328640-117502785	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv893766	chr9:117385992-117516418	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1042718	chr9:117435306-117488969	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11793753	EPCAM	trans	brain	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117457600-117462200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr9:117458800-117460200	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr9:117458800-117460400	Enhancers	Primary T cells fromperipheralblood	blood
4	chr9:117458800-117460400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr9:117458800-117460600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr9:117458800-117461000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:117459000-117460200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:117459000-117460200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:117459000-117460200	Enhancers	NHDF-Ad	bronchial
10	chr9:117459000-117460400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr9:117459000-117461000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:117459200-117460400	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr9:117459400-117460200	Enhancers	HMEC	breast
14	chr9:117459600-117460200	Enhancers	Hela-S3	cervix
15	chr9:117459800-117460600	Flanking Active TSS	GM12878-XiMat	blood
16	chr9:117460000-117460200	Enhancers	Small Intestine	intestine
17	chr9:117460000-117462200	Weak transcription	NHEK	skin
18	chr9:117460000-117463800	Weak transcription	HSMM	muscle
19	chr9:117460000-117464000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:117460000-117464400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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