Variant report

Variant	rs12816390
Chromosome Location	chr12:9425900-9425901
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	STAT3	chr12:9425856-9426303	MCF10A-Er-Src	breast:	n/a	chr12:9426078-9426087
2	GATA3	chr12:9425689-9426511	MCF-7	breast:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023
3	SIN3AK20	chr12:9425584-9426335	MCF-7	breast:	n/a	n/a
4	JUND	chr12:9425772-9426299	MCF-7	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
5	GATA3	chr12:9425669-9426353	MCF-7	breast:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023
6	KAP1	chr12:9425619-9426401	HEK293	kidney:	n/a	chr12:9426076-9426085
7	FOS	chr12:9425893-9426460	MCF10A-Er-Src	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
8	CEBPB	chr12:9425769-9426325	MCF-7	breast:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
9	JUND	chr12:9425632-9426529	Hela-S3	cervix:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
10	STAT3	chr12:9425864-9426254	MCF10A-Er-Src	breast:	n/a	chr12:9426078-9426087
11	CEBPB	chr12:9425770-9426296	MCF-7	breast:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
12	FOS	chr12:9425749-9426514	MCF10A-Er-Src	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
13	CEBPB	chr12:9425858-9426344	A549	lung:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
14	ZNF217	chr12:9425519-9426374	MCF-7	breast:	n/a	n/a
15	GATA3	chr12:9425886-9426186	SK-N-SH	brain:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023
16	NR2F2	chr12:9425687-9426172	MCF-7	breast:	n/a	n/a
17	GATA3	chr12:9425651-9426209	MCF-7	breast:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023
18	EP300	chr12:9425749-9426516	Hela-S3	cervix:	n/a	chr12:9426089-9426103 chr12:9426292-9426306 chr12:9426077-9426086
19	CEBPB	chr12:9425540-9426480	Hela-S3	cervix:	n/a	chr12:9426088-9426101 chr12:9426088-9426099
20	FOS	chr12:9425864-9426365	MCF10A-Er-Src	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
21	NR2F2	chr12:9425804-9426284	MCF-7	breast:	n/a	n/a
22	STAT3	chr12:9425647-9426769	Hela-S3	cervix:	n/a	chr12:9426078-9426087
23	KAP1	chr12:9425739-9426448	U2OS	brain:	n/a	chr12:9426076-9426085
24	FOS	chr12:9425818-9426240	Hela-S3	cervix:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
25	RAD21	chr12:9425653-9426389	Hela-S3	cervix:	n/a	n/a
26	FOSL2	chr12:9425784-9426227	MCF-7	breast:	n/a	chr12:9426076-9426088 chr12:9426077-9426086 chr12:9426078-9426087
27	JUN	chr12:9425552-9426473	Hela-S3	cervix:	n/a	chr12:9426076-9426088 chr12:9426077-9426086 chr12:9426078-9426087 chr12:9426089-9426102
28	MYC	chr12:9425887-9426532	MCF10A-Er-Src	breast:	n/a	chr12:9426310-9426320 chr12:9426091-9426100 chr12:9426077-9426086 chr12:9426311-9426321
29	TCF7L2	chr12:9425721-9426287	Hela-S3	cervix:	n/a	chr12:9426078-9426087 chr12:9426077-9426086
30	RFX5	chr12:9425433-9426386	Hela-S3	cervix:	n/a	n/a
31	JUND	chr12:9425783-9426331	MCF-7	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
32	FOS	chr12:9425665-9426459	MCF10A-Er-Src	breast:	n/a	chr12:9426076-9426088 chr12:9426076-9426087 chr12:9426077-9426086 chr12:9426078-9426087
33	USF2	chr12:9425708-9426270	Hela-S3	cervix:	n/a	n/a
34	HDAC2	chr12:9425807-9426284	MCF-7	breast:	n/a	n/a
35	TCF7L2	chr12:9425895-9426218	MCF-7	breast:	n/a	chr12:9426078-9426087 chr12:9426077-9426086
36	MYC	chr12:9425847-9426505	MCF10A-Er-Src	breast:	n/a	chr12:9426310-9426320 chr12:9426091-9426100 chr12:9426077-9426086 chr12:9426311-9426321
37	RCOR1	chr12:9425724-9426394	Hela-S3	cervix:	n/a	n/a
38	GATA3	chr12:9425800-9426239	MCF-7	breast:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023
39	GATA3	chr12:9425590-9426370	A549	lung:	n/a	chr12:9425974-9425981 chr12:9426010-9426019 chr12:9425973-9425981 chr12:9426007-9426023
40	FOXM1	chr12:9425660-9426384	MCF-7	breast:	n/a	n/a
41	BRCA1	chr12:9425592-9426520	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9423398..9426359-chr12:9434637..9436174,2	K562	blood:
2	chr12:9423490..9426134-chr12:9432405..9434234,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111788	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10771440	0.88[EUR][1000 genomes]
rs10771443	0.88[EUR][1000 genomes]
rs10771445	0.90[EUR][1000 genomes]
rs10843242	0.91[EUR][1000 genomes]
rs10843243	0.91[EUR][1000 genomes]
rs10843244	0.91[EUR][1000 genomes]
rs11049800	0.83[EUR][1000 genomes]
rs11049844	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11611191	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12579180	0.84[EUR][1000 genomes]
rs12581534	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815281	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822417	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12824461	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs187536	0.91[EUR][1000 genomes]
rs194037	0.91[EUR][1000 genomes]
rs2059760	0.88[EUR][1000 genomes]
rs2059761	0.88[EUR][1000 genomes]
rs252019	0.87[EUR][1000 genomes]
rs252027	0.91[EUR][1000 genomes]
rs252028	0.91[EUR][1000 genomes]
rs252029	0.91[EUR][1000 genomes]
rs252030	0.91[EUR][1000 genomes]
rs252032	0.91[EUR][1000 genomes]
rs252033	0.91[EUR][1000 genomes]
rs34332	0.88[EUR][1000 genomes]
rs34333	0.88[EUR][1000 genomes]
rs34334	0.88[EUR][1000 genomes]
rs34856550	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4883225	0.86[EUR][1000 genomes]
rs4883226	0.92[EUR][1000 genomes]
rs55913537	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56288591	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61916195	0.82[AMR][1000 genomes]
rs7299846	0.88[EUR][1000 genomes]
rs7309684	0.83[EUR][1000 genomes]
rs7316531	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7958291	0.88[EUR][1000 genomes]
rs7967738	0.92[EUR][1000 genomes]
rs7974378	0.88[EUR][1000 genomes]
rs7976100	0.88[EUR][1000 genomes]
rs7980256	0.92[EUR][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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12816390	DDX12P	cis	Nerve Tibial	GTEx
rs12816390	RP11-22B23.1	cis	Whole Blood	GTEx
rs12816390	RP11-22B23.1	cis	lung	GTEx
rs12816390	A2MP1	cis	Adipose Subcutaneous	GTEx
rs12816390	RP11-22B23.1	cis	Esophagus Muscularis	GTEx
rs12816390	RP11-22B23.1	cis	Nerve Tibial	GTEx
rs12816390	RP11-22B23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs12816390	DDX12P	cis	Thyroid	GTEx
rs12816390	DDX12P	cis	Muscle Skeletal	GTEx
rs12816390	RP11-22B23.1	cis	Thyroid	GTEx
rs12816390	DDX12P	cis	Artery Tibial	GTEx
rs12816390	SNORA75	cis	lung	GTEx
rs12816390	RP11-22B23.1	cis	Artery Tibial	GTEx
rs12816390	A2MP1	cis	Nerve Tibial	GTEx
rs12816390	RP11-22B23.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9425600-9426000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:9425600-9426000	Flanking Active TSS	Hela-S3	cervix
3	chr12:9425600-9426400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr12:9425600-9427000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:9425600-9427000	Enhancers	HMEC	breast
6	chr12:9425800-9426000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:9425800-9426200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:9425800-9426400	Enhancers	NHEK	skin
9	chr12:9425800-9426400	Enhancers	Osteobl	bone
10	chr12:9425800-9426800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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