Variant report

Variant	rs11049928
Chromosome Location	chr12:9426171-9426172
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	CEBPB	chr12:9425943-9426247	K562	blood:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
2	STAT3	chr12:9425856-9426303	MCF10A-Er-Src	breast:	n/a	chr12:9426078-9426087
3	GATA3	chr12:9425689-9426511	MCF-7	breast:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023
4	SIN3AK20	chr12:9425584-9426335	MCF-7	breast:	n/a	n/a
5	JUND	chr12:9425915-9426278	HepG2	liver:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
6	JUND	chr12:9425772-9426299	MCF-7	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
7	GATA3	chr12:9425669-9426353	MCF-7	breast:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023
8	KAP1	chr12:9425619-9426401	HEK293	kidney:	n/a	chr12:9426076-9426085
9	FOS	chr12:9425893-9426460	MCF10A-Er-Src	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
10	CEBPB	chr12:9425769-9426325	MCF-7	breast:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
11	JUN	chr12:9425930-9426246	HepG2	liver:	n/a	chr12:9426076-9426088 chr12:9426077-9426086 chr12:9426078-9426087 chr12:9426089-9426102
12	JUND	chr12:9425632-9426529	Hela-S3	cervix:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
13	STAT3	chr12:9425864-9426254	MCF10A-Er-Src	breast:	n/a	chr12:9426078-9426087
14	FOS	chr12:9425912-9426202	HUVEC	blood vessel:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
15	CEBPB	chr12:9425770-9426296	MCF-7	breast:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
16	FOS	chr12:9425749-9426514	MCF10A-Er-Src	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
17	CEBPB	chr12:9425858-9426344	A549	lung:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
18	ZNF217	chr12:9425519-9426374	MCF-7	breast:	n/a	n/a
19	GATA3	chr12:9425886-9426186	SK-N-SH	brain:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023
20	NR2F2	chr12:9425687-9426172	MCF-7	breast:	n/a	n/a
21	JUND	chr12:9425942-9426248	K562	blood:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
22	GATA3	chr12:9425651-9426209	MCF-7	breast:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023
23	EP300	chr12:9425749-9426516	Hela-S3	cervix:	n/a	chr12:9426089-9426103 chr12:9426292-9426306 chr12:9426077-9426086
24	CEBPB	chr12:9425540-9426480	Hela-S3	cervix:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
25	FOS	chr12:9425864-9426365	MCF10A-Er-Src	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
26	CEBPB	chr12:9425901-9426291	IMR90	lung:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
27	NR2F2	chr12:9425804-9426284	MCF-7	breast:	n/a	n/a
28	CEBPB	chr12:9425969-9426267	A549	lung:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
29	STAT3	chr12:9425911-9426221	MCF10A-Er-Src	breast:	n/a	chr12:9426078-9426087
30	STAT3	chr12:9425647-9426769	Hela-S3	cervix:	n/a	chr12:9426078-9426087
31	POLR2A	chr12:9426136-9426608	MCF10A-Er-Src	breast:	n/a	n/a
32	CEBPB	chr12:9425959-9426175	HepG2	liver:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
33	KAP1	chr12:9425739-9426448	U2OS	brain:	n/a	chr12:9426076-9426085
34	FOS	chr12:9425818-9426240	Hela-S3	cervix:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
35	RAD21	chr12:9425653-9426389	Hela-S3	cervix:	n/a	n/a
36	FOSL2	chr12:9425784-9426227	MCF-7	breast:	n/a	chr12:9426076-9426088 chr12:9426077-9426086 chr12:9426078-9426087
37	JUN	chr12:9425552-9426473	Hela-S3	cervix:	n/a	chr12:9426076-9426088 chr12:9426077-9426086 chr12:9426078-9426087 chr12:9426089-9426102
38	POLR2A	chr12:9426064-9427230	MCF10A-Er-Src	breast:	n/a	n/a
39	MYC	chr12:9425887-9426532	MCF10A-Er-Src	breast:	n/a	chr12:9426310-9426320 chr12:9426091-9426100 chr12:9426077-9426086 chr12:9426311-9426321
40	TCF7L2	chr12:9425721-9426287	Hela-S3	cervix:	n/a	chr12:9426078-9426087 chr12:9426077-9426086
41	RFX5	chr12:9425433-9426386	Hela-S3	cervix:	n/a	n/a
42	JUND	chr12:9425783-9426331	MCF-7	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
43	FOS	chr12:9425665-9426459	MCF10A-Er-Src	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
44	STAT3	chr12:9425977-9426336	MCF10A-Er-Src	breast:	n/a	chr12:9426078-9426087
45	USF2	chr12:9425708-9426270	Hela-S3	cervix:	n/a	n/a
46	HDAC2	chr12:9425807-9426284	MCF-7	breast:	n/a	n/a
47	TCF7L2	chr12:9425895-9426218	MCF-7	breast:	n/a	chr12:9426078-9426087 chr12:9426077-9426086
48	MYC	chr12:9425847-9426505	MCF10A-Er-Src	breast:	n/a	chr12:9426310-9426320 chr12:9426091-9426100 chr12:9426077-9426086 chr12:9426311-9426321
49	RCOR1	chr12:9425724-9426394	Hela-S3	cervix:	n/a	n/a
50	GATA3	chr12:9425800-9426239	MCF-7	breast:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9423398..9426359-chr12:9434637..9436174,2	K562	blood:

Variant related genes	Relation type
ENSG00000111788	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2377756	1.00[CEU][hapmap]
rs2429893	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs6487733	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv527404	chr12:9250601-9435244	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
7	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
8	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
10	nsv1048917	chr12:9393282-9436132	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv898739	chr12:9398365-9435244	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv983234	chr12:9416478-9431362	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv983481	chr12:9423000-9426898	Flanking Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11049928	RP11-22B23.1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9425600-9426400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr12:9425600-9427000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:9425600-9427000	Enhancers	HMEC	breast
4	chr12:9425800-9426200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:9425800-9426400	Enhancers	NHEK	skin
6	chr12:9425800-9426400	Enhancers	Osteobl	bone
7	chr12:9425800-9426800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:9426000-9426400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:9426000-9427400	Enhancers	Hela-S3	cervix

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