Variant report

Variant	rs12818241
Chromosome Location	chr12:48157019-48157020
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	ESR1	chr12:48156717-48157901	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr12:48156556-48158088	ECC-1	luminal epithelium:	n/a	chr12:48157434-48157450
3	TCF12	chr12:48156309-48158310	ECC-1	luminal epithelium:	n/a	chr12:48157158-48157168 chr12:48157160-48157167 chr12:48156566-48156576 chr12:48157581-48157591
4	GATA3	chr12:48156506-48157235	SH-SY5Y	brain:	n/a	chr12:48156881-48156888
5	POLR2A	chr12:48156439-48158112	ECC-1	luminal epithelium:	n/a	n/a
6	FOXM1	chr12:48156467-48158154	ECC-1	luminal epithelium:	n/a	n/a
7	ZBTB7A	chr12:48156967-48158246	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr12:48156639-48158163	ECC-1	luminal epithelium:	n/a	n/a
9	NFIC	chr12:48156632-48158182	ECC-1	luminal epithelium:	n/a	chr12:48157459-48157476
10	POLR2A	chr12:48156574-48158056	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr12:48156464-48158154	ECC-1	luminal epithelium:	n/a	chr12:48157158-48157168 chr12:48157160-48157167 chr12:48156566-48156576 chr12:48157581-48157591
12	TEAD4	chr12:48156492-48158011	ECC-1	luminal epithelium:	n/a	chr12:48157664-48157673
13	NFIC	chr12:48156470-48158288	ECC-1	luminal epithelium:	n/a	chr12:48157459-48157476
14	MAX	chr12:48156818-48158129	ECC-1	luminal epithelium:	n/a	n/a
15	EP300	chr12:48155606-48158295	ECC-1	luminal epithelium:	n/a	chr12:48156128-48156141 chr12:48157434-48157450
16	EP300	chr12:48156259-48157886	SK-N-SH	brain:	n/a	chr12:48157434-48157450
17	FOXM1	chr12:48156493-48158118	ECC-1	luminal epithelium:	n/a	n/a
18	TEAD4	chr12:48156397-48158135	ECC-1	luminal epithelium:	n/a	chr12:48157664-48157673
19	GATA2	chr12:48156188-48157473	SH-SY5Y	brain:	n/a	chr12:48156881-48156888

No.	Distal block	Cell Line	Cell type
1	chr12:48145090..48147406-chr12:48155481..48157824,2	K562	blood:
2	chr12:48155062..48157488-chr12:48222894..48224930,2	K562	blood:
3	chr12:48151483..48157972-chr12:48164331..48169743,9	K562	blood:
4	chr12:48134751..48136933-chr12:48155873..48158098,2	K562	blood:
5	chr12:48098197..48100368-chr12:48154682..48157189,2	K562	blood:
6	chr12:48144320..48146490-chr12:48155859..48158301,2	MCF-7	breast:
7	chr12:48156301..48158741-chr12:48170596..48173234,2	MCF-7	breast:
8	chr12:48140094..48143187-chr12:48155168..48157546,4	K562	blood:
9	chr12:48142143..48143879-chr12:48156627..48159183,2	MCF-7	breast:

Variant related genes	Relation type
RAPGEF3	TF binding region
ENSG00000005175	Chromatin interaction
ENSG00000257488	Chromatin interaction
ENSG00000257433	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12422983	0.84[TSI][hapmap];0.85[AMR][1000 genomes]
rs12423645	1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs12424297	0.85[AMR][1000 genomes]
rs12426774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12810487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815308	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12815462	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12817548	0.87[AMR][1000 genomes]
rs12818212	1.00[CHB][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes]
rs12818990	0.81[ASN][1000 genomes]
rs12825831	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831651	0.93[EUR][1000 genomes]
rs2283345	0.85[CEU][hapmap]
rs4340112	1.00[JPT][hapmap]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12818241	RAPGEF3	cis	cerebellum	SCAN
rs12818241	TMEM117	cis	cerebellum	SCAN
rs12818241	DDX23	cis	parietal	SCAN
rs12818241	RAPGEF3	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48153400-48159200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:48153400-48161800	Weak transcription	Aorta	Aorta
3	chr12:48153600-48157200	Weak transcription	Pancreas	Pancrea
4	chr12:48153600-48157200	Weak transcription	Right Atrium	heart
5	chr12:48153600-48157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:48153600-48157400	Weak transcription	Fetal Lung	lung
7	chr12:48153600-48157400	Weak transcription	GM12878-XiMat	blood
8	chr12:48153600-48159000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48153600-48159400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:48153600-48159800	Weak transcription	Brain Germinal Matrix	brain
11	chr12:48153600-48161000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:48153600-48161200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:48153600-48161200	Weak transcription	NHDF-Ad	bronchial
14	chr12:48153600-48162000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr12:48153600-48162200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:48153600-48162800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:48153600-48166000	Weak transcription	Brain Angular Gyrus	brain
18	chr12:48153600-48166200	Weak transcription	Brain Anterior Caudate	brain
19	chr12:48153600-48166400	Weak transcription	Fetal Brain Female	brain
20	chr12:48153600-48166800	Weak transcription	Gastric	stomach
21	chr12:48153800-48157200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:48153800-48157200	Weak transcription	Adipose Nuclei	Adipose
23	chr12:48153800-48157200	Weak transcription	Fetal Stomach	stomach
24	chr12:48153800-48157400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:48153800-48157600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr12:48153800-48157600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:48153800-48161400	Weak transcription	K562	blood
28	chr12:48153800-48162000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:48153800-48162200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:48153800-48165600	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:48153800-48165800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:48153800-48166200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:48154000-48157200	Weak transcription	Primary B cells from cord blood	blood
34	chr12:48154200-48157200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:48154200-48157600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:48154200-48161200	Weak transcription	A549	lung
37	chr12:48154200-48161200	Weak transcription	Hela-S3	cervix
38	chr12:48154400-48157200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:48154400-48157200	Weak transcription	Esophagus	oesophagus
40	chr12:48154400-48157200	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:48154400-48159000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:48154400-48159400	Weak transcription	Colon Smooth Muscle	Colon
43	chr12:48154400-48165800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:48154600-48157200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:48155600-48157400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:48155800-48157800	Enhancers	Ovary	ovary
47	chr12:48155800-48159200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:48156000-48157800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:48156000-48158200	Enhancers	Fetal Kidney	kidney
50	chr12:48156200-48157200	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links