Variant report

Variant	rs74088046
Chromosome Location	chr12:48146725-48146726
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	EP300	chr12:48146238-48148408	SK-N-SH	brain:	n/a	chr12:48147400-48147414
2	STAT3	chr12:48146319-48146735	MCF10A-Er-Src	breast:	n/a	chr12:48146549-48146560
3	FOS	chr12:48146293-48146766	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr12:48146292-48146727	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr12:48146321-48146736	MCF10A-Er-Src	breast:	n/a	chr12:48146549-48146560
6	STAT3	chr12:48146420-48146738	MCF10A-Er-Src	breast:	n/a	chr12:48146549-48146560
7	FOS	chr12:48146309-48146738	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr12:48146293-48146735	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr12:48146302-48146819	MCF10A-Er-Src	breast:	n/a	chr12:48146549-48146560
10	POLR2A	chr12:48146426-48148248	Hela-S3	cervix:	n/a	n/a
11	SMARCC1	chr12:48146110-48149011	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:48146395-48149013	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48139218..48143283-chr12:48146093..48149337,5	K562	blood:
2	chr12:48146163..48148373-chr12:48150555..48153521,2	K562	blood:
3	chr12:48145973..48147793-chr12:48165632..48167203,2	MCF-7	breast:
4	chr12:48146517..48147373-chr19:1173092..1174043,2	Hela-S3	cervix:
5	chr12:48145090..48147406-chr12:48155481..48157824,2	K562	blood:
6	chr12:48144826..48150380-chr12:48164026..48173211,11	K562	blood:
7	chr12:48146667..48149507-chr12:48298293..48300492,2	MCF-7	breast:
8	chr12:48144391..48147829-chr12:48212557..48216683,4	MCF-7	breast:

Variant related genes	Relation type
RAPGEF3	TF binding region
SLC48A1	TF binding region
ENSG00000079337	Chromatin interaction
ENSG00000064932	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11168194	0.85[EUR][1000 genomes]
rs3764014	0.85[EUR][1000 genomes]
rs73304406	0.85[ASN][1000 genomes]
rs74088038	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][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:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:48134800-48147000	Weak transcription	Psoas Muscle	Psoas
3	chr12:48135400-48147000	Weak transcription	Colonic Mucosa	Colon
4	chr12:48135400-48147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:48135600-48148000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:48136000-48147400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:48138000-48148000	Weak transcription	Liver	Liver
8	chr12:48139400-48147000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:48139800-48146800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:48140200-48146800	Weak transcription	Fetal Heart	heart
11	chr12:48141200-48147600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:48141600-48147000	Weak transcription	GM12878-XiMat	blood
13	chr12:48141800-48147000	Weak transcription	Primary B cells from cord blood	blood
14	chr12:48143200-48147000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:48144200-48146800	Enhancers	HMEC	breast
16	chr12:48144200-48150000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:48144200-48150200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:48144200-48151000	Weak transcription	Brain Germinal Matrix	brain
19	chr12:48144800-48146800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:48144800-48147400	Weak transcription	Fetal Kidney	kidney
21	chr12:48145000-48149000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:48145200-48146800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr12:48145200-48147000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr12:48145200-48148600	Genic enhancers	Brain Hippocampus Middle	brain
25	chr12:48145200-48148600	Enhancers	Esophagus	oesophagus
26	chr12:48145200-48149000	Enhancers	HSMM	muscle
27	chr12:48145400-48147200	Weak transcription	Pancreas	Pancrea
28	chr12:48145400-48148400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr12:48145400-48148400	Genic enhancers	Brain Cingulate Gyrus	brain
30	chr12:48145400-48148800	Enhancers	Left Ventricle	heart
31	chr12:48145400-48150800	Enhancers	NHDF-Ad	bronchial
32	chr12:48145400-48151400	Enhancers	Placenta	Placenta
33	chr12:48145600-48147800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:48145600-48147800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr12:48145600-48148400	Enhancers	A549	lung
36	chr12:48145600-48149600	Enhancers	Lung	lung
37	chr12:48145600-48149800	Enhancers	HSMMtube	muscle
38	chr12:48145600-48150000	Enhancers	Fetal Muscle Trunk	muscle
39	chr12:48145600-48150200	Enhancers	Placenta Amnion	Placenta Amnion
40	chr12:48145600-48150800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr12:48145600-48151000	Enhancers	Spleen	Spleen
42	chr12:48145800-48147400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr12:48145800-48147400	Enhancers	Stomach Smooth Muscle	stomach
44	chr12:48145800-48148000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:48145800-48148200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:48145800-48148200	Enhancers	NHLF	lung
47	chr12:48145800-48148600	Enhancers	Brain Anterior Caudate	brain
48	chr12:48145800-48151200	Enhancers	Gastric	stomach
49	chr12:48146000-48147200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:48146000-48147400	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links