Variant report

Variant	rs73105873
Chromosome Location	chr12:48148700-48148701
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	TCF12	chr12:48146913-48149199	ECC-1	luminal epithelium:	n/a	chr12:48147111-48147121
2	HDAC2	chr12:48148562-48148969	MCF-7	breast:	n/a	n/a
3	RUNX3	chr12:48148641-48149985	GM12878	blood:	n/a	chr12:48148819-48148834
4	POLR2A	chr12:48148641-48148796	Hela-S3	cervix:	n/a	n/a
5	WRNIP1	chr12:48148665-48149597	GM12878	blood:	n/a	n/a
6	NFIC	chr12:48148362-48149226	ECC-1	luminal epithelium:	n/a	n/a
7	MTA3	chr12:48148435-48149970	GM12878	blood:	n/a	n/a
8	NR2F2	chr12:48148475-48149102	MCF-7	breast:	n/a	n/a
9	TFAP2C	chr12:48146933-48149021	Hela-S3	cervix:	n/a	chr12:48147383-48147398 chr12:48148785-48148800
10	POLR2A	chr12:48148456-48149078	ECC-1	luminal epithelium:	n/a	n/a
11	MAX	chr12:48148647-48148966	GM12878	blood:	n/a	n/a
12	NR3C1	chr12:48148505-48148970	ECC-1	luminal epithelium:	n/a	chr12:48148610-48148623
13	EP300	chr12:48148642-48149887	GM12878	blood:	n/a	chr12:48148703-48148716
14	TFAP2A	chr12:48147065-48148946	Hela-S3	cervix:	n/a	chr12:48148068-48148079 chr12:48147301-48147316 chr12:48148068-48148079 chr12:48148154-48148169 chr12:48148068-48148079 chr12:48148068-48148079
15	NR3C1	chr12:48148497-48148920	ECC-1	luminal epithelium:	n/a	chr12:48148610-48148623
16	MAX	chr12:48148448-48149161	ECC-1	luminal epithelium:	n/a	n/a
17	EBF1	chr12:48148583-48150102	GM12878	blood:	n/a	chr12:48148786-48148797
18	ZNF143	chr12:48148516-48148802	Hela-S3	cervix:	n/a	n/a
19	EP300	chr12:48148416-48149156	ECC-1	luminal epithelium:	n/a	chr12:48148610-48148623 chr12:48148703-48148716
20	EBF1	chr12:48148592-48149042	GM12878	blood:	n/a	chr12:48148786-48148797
21	NFIC	chr12:48146866-48149274	ECC-1	luminal epithelium:	n/a	chr12:48147611-48147639
22	TCF12	chr12:48148416-48149177	ECC-1	luminal epithelium:	n/a	n/a
23	ESR1	chr12:48148555-48148958	ECC-1	luminal epithelium:	n/a	n/a
24	MAX	chr12:48148442-48149050	MCF-7	breast:	n/a	n/a
25	RELA	chr12:48148609-48150014	GM18951	blood:	n/a	n/a
26	GTF2F1	chr12:48148606-48148744	Hela-S3	cervix:	n/a	n/a
27	EP300	chr12:48146839-48150642	ECC-1	luminal epithelium:	n/a	chr12:48148610-48148623 chr12:48147400-48147414 chr12:48148703-48148716
28	ZKSCAN1	chr12:48148674-48148784	Hela-S3	cervix:	n/a	n/a
29	RFX5	chr12:48148665-48149010	GM12878	blood:	n/a	n/a
30	MAX	chr12:48148438-48149189	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr12:48148574-48148854	HCT-116	colon:	n/a	n/a
32	SMARCC1	chr12:48146110-48149011	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:48146395-48149013	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr12:48148568-48148897	HCT-116	colon:	n/a	n/a
35	MAZ	chr12:48148589-48148821	Hela-S3	cervix:	n/a	n/a
36	ZNF217	chr12:48148588-48148876	MCF-7	breast:	n/a	n/a
37	ESR1	chr12:48148438-48148974	ECC-1	luminal epithelium:	n/a	n/a
38	RUNX3	chr12:48148637-48150045	GM12878	blood:	n/a	chr12:48148819-48148834
39	PML	chr12:48148668-48149909	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48139218..48143283-chr12:48146093..48149337,5	K562	blood:
2	chr12:48135061..48136993-chr12:48147045..48149552,2	MCF-7	breast:
3	chr12:48147317..48148897-chr12:48163637..48165768,2	MCF-7	breast:
4	chr12:48144826..48150380-chr12:48164026..48173211,11	K562	blood:
5	chr12:48146667..48149507-chr12:48298293..48300492,2	MCF-7	breast:

Variant related genes	Relation type
RAPGEF3	TF binding region
SLC48A1	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000111424	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11608637	1.00[AMR][1000 genomes]
rs12721361	1.00[AMR][1000 genomes]
rs73107974	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48144200-48150000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:48144200-48150200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:48144200-48151000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:48145000-48149000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:48145200-48149000	Enhancers	HSMM	muscle
6	chr12:48145400-48148800	Enhancers	Left Ventricle	heart
7	chr12:48145400-48150800	Enhancers	NHDF-Ad	bronchial
8	chr12:48145400-48151400	Enhancers	Placenta	Placenta
9	chr12:48145600-48149600	Enhancers	Lung	lung
10	chr12:48145600-48149800	Enhancers	HSMMtube	muscle
11	chr12:48145600-48150000	Enhancers	Fetal Muscle Trunk	muscle
12	chr12:48145600-48150200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr12:48145600-48150800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:48145600-48151000	Enhancers	Spleen	Spleen
15	chr12:48145800-48151200	Enhancers	Gastric	stomach
16	chr12:48146000-48149200	Enhancers	Right Atrium	heart
17	chr12:48146000-48149400	Enhancers	Right Ventricle	heart
18	chr12:48146000-48151400	Enhancers	Stomach Mucosa	stomach
19	chr12:48146200-48148800	Enhancers	Osteobl	bone
20	chr12:48146200-48149400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:48146200-48150200	Enhancers	Fetal Muscle Leg	muscle
22	chr12:48146400-48148800	Enhancers	Brain Angular Gyrus	brain
23	chr12:48146600-48148800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:48146600-48149000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:48146600-48149000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:48146600-48149000	Enhancers	Aorta	Aorta
27	chr12:48146600-48149000	Flanking Active TSS	Hela-S3	cervix
28	chr12:48146600-48149400	Enhancers	Fetal Lung	lung
29	chr12:48146600-48150400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:48146800-48148800	Flanking Active TSS	HMEC	breast
31	chr12:48147000-48149200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:48147000-48149400	Enhancers	Colonic Mucosa	Colon
33	chr12:48147000-48150400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:48147000-48151800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:48147000-48152200	Enhancers	Primary B cells from peripheral blood	blood
36	chr12:48147000-48152400	Enhancers	Primary B cells from cord blood	blood
37	chr12:48147000-48152400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr12:48147200-48150400	Enhancers	Pancreas	Pancrea
39	chr12:48147200-48150800	Enhancers	Ovary	ovary
40	chr12:48147400-48148800	Enhancers	Fetal Kidney	kidney
41	chr12:48147600-48150000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:48147600-48150000	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr12:48147600-48151400	Weak transcription	Fetal Intestine Large	intestine
44	chr12:48147800-48148800	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr12:48147800-48149400	Weak transcription	Fetal Intestine Small	intestine
46	chr12:48147800-48149600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr12:48147800-48149600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr12:48147800-48149800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr12:48147800-48150000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:48147800-48150200	Enhancers	Small Intestine	intestine

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