Variant report

Variant	rs56907417
Chromosome Location	chr12:48151024-48151025
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	TCF12	chr12:48149292-48153761	ECC-1	luminal epithelium:	n/a	chr12:48151904-48151914 chr12:48153083-48153090 chr12:48152062-48152069 chr12:48149639-48149646 chr12:48152628-48152635 chr12:48152630-48152637
2	TCF12	chr12:48150887-48153727	ECC-1	luminal epithelium:	n/a	chr12:48151904-48151914 chr12:48153083-48153090 chr12:48152062-48152069 chr12:48152628-48152635 chr12:48152630-48152637
3	EP300	chr12:48150750-48153828	ECC-1	luminal epithelium:	n/a	chr12:48153612-48153626 chr12:48153099-48153115 chr12:48152632-48152648 chr12:48152971-48152981 chr12:48153189-48153205
4	TEAD4	chr12:48150874-48153703	ECC-1	luminal epithelium:	n/a	n/a
5	YY1	chr12:48150895-48153399	ECC-1	luminal epithelium:	n/a	chr12:48153191-48153202 chr12:48152736-48152745 chr12:48152730-48152739
6	ZBTB7A	chr12:48150947-48153704	ECC-1	luminal epithelium:	n/a	chr12:48151147-48151161
7	MAX	chr12:48151006-48153797	ECC-1	luminal epithelium:	n/a	chr12:48152950-48152963 chr12:48151248-48151257 chr12:48152952-48152961 chr12:48152951-48152962 chr12:48152734-48152744 chr12:48152952-48152962 chr12:48152952-48152962

No.	Distal block	Cell Line	Cell type
1	chr12:48149372..48151812-chr12:48213789..48216551,2	MCF-7	breast:
2	chr12:48146163..48148373-chr12:48150555..48153521,2	K562	blood:
3	chr12:48149008..48151227-chr12:48151474..48154219,4	K562	blood:
4	chr12:48136067..48137625-chr12:48149838..48151816,2	K562	blood:
5	chr12:48143654..48145769-chr12:48149480..48151758,2	K562	blood:

Variant related genes	Relation type
SLC48A1	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs61275291	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61709815	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7134842	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73302698	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv518315	chr12:48149752-48152995	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48145400-48151400	Enhancers	Placenta	Placenta
2	chr12:48145800-48151200	Enhancers	Gastric	stomach
3	chr12:48146000-48151400	Enhancers	Stomach Mucosa	stomach
4	chr12:48147000-48151800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:48147000-48152200	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:48147000-48152400	Enhancers	Primary B cells from cord blood	blood
7	chr12:48147000-48152400	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr12:48147600-48151400	Weak transcription	Fetal Intestine Large	intestine
9	chr12:48147800-48151400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:48148000-48151400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:48148000-48151600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:48148000-48151800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:48148000-48152200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:48148200-48151200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr12:48148200-48151200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:48148200-48151200	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:48148200-48151400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:48148200-48151400	Weak transcription	NHLF	lung
19	chr12:48148400-48151200	Weak transcription	NH-A	brain
20	chr12:48148400-48151400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:48148400-48152000	Weak transcription	A549	lung
22	chr12:48148400-48152200	Enhancers	Fetal Thymus	thymus
23	chr12:48148800-48151200	Weak transcription	Fetal Brain Male	brain
24	chr12:48148800-48151200	Weak transcription	Osteobl	bone
25	chr12:48148800-48151400	Active TSS	Stomach Smooth Muscle	stomach
26	chr12:48148800-48151400	Enhancers	HMEC	breast
27	chr12:48148800-48152200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:48149000-48151200	Weak transcription	Fetal Stomach	stomach
29	chr12:48149000-48151200	Weak transcription	HSMM	muscle
30	chr12:48149000-48151600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:48149000-48152200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:48149000-48153800	Active TSS	Psoas Muscle	Psoas
33	chr12:48149400-48151200	Enhancers	Primary hematopoietic stem cells	blood
34	chr12:48149400-48151200	Weak transcription	Fetal Lung	lung
35	chr12:48149400-48151400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:48149400-48151400	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr12:48149400-48152400	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr12:48149800-48151200	Weak transcription	Liver	Liver
39	chr12:48149800-48151200	Weak transcription	Fetal Heart	heart
40	chr12:48149800-48151200	Weak transcription	HSMMtube	muscle
41	chr12:48149800-48151800	Weak transcription	Fetal Intestine Small	intestine
42	chr12:48149800-48152000	Weak transcription	Aorta	Aorta
43	chr12:48149800-48153200	Active TSS	Left Ventricle	heart
44	chr12:48149800-48153600	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr12:48150000-48151200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:48150000-48151400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr12:48150000-48151600	Active TSS	Adipose Nuclei	Adipose
48	chr12:48150000-48151800	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr12:48150000-48152000	Weak transcription	K562	blood
50	chr12:48150000-48152200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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