Variant report

Variant	rs3809193
Chromosome Location	chr12:117176705-117176706
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	RFX5	chr12:117174654-117177903	SK-N-SH	brain:	n/a	chr12:117174964-117174973 chr12:117174962-117174976 chr12:117176118-117176127
2	TCF7L2	chr12:117176250-117176713	HEK293	kidney:	n/a	chr12:117176441-117176448 chr12:117176436-117176450 chr12:117176440-117176449
3	MAX	chr12:117175459-117176772	A549	lung:	n/a	chr12:117175865-117175874 chr12:117176692-117176702 chr12:117175863-117175872 chr12:117175864-117175875
4	POLR2A	chr12:117175568-117176727	GM12891	blood:	n/a	n/a
5	SIN3AK20	chr12:117175365-117176794	MCF-7	breast:	n/a	n/a
6	MXI1	chr12:117174549-117177000	SK-N-SH	brain:	n/a	chr12:117175866-117175875
7	REST	chr12:117175397-117176888	H1-neurons	neurons:	n/a	chr12:117176100-117176113
8	HCFC1	chr12:117175455-117177226	Hela-S3	cervix:	n/a	n/a
9	RCOR1	chr12:117175475-117176738	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:117172847..117175842-chr12:117176495..117179141,3	MCF-7	breast:
2	chr12:117174783..117176988-chr12:117316113..117318785,2	MCF-7	breast:
3	chr12:117155749..117159803-chr12:117174359..117177084,5	MCF-7	breast:

Variant related genes	Relation type
C12orf49	TF binding region
ENSG00000111412	Chromatin interaction
ENSG00000135116	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11832933	0.83[EUR][1000 genomes]
rs11833612	0.83[EUR][1000 genomes]
rs11835089	0.83[EUR][1000 genomes]
rs11835957	0.83[EUR][1000 genomes]
rs11835971	0.83[EUR][1000 genomes]
rs17616249	0.83[EUR][1000 genomes]
rs35412759	0.83[EUR][1000 genomes]
rs3809191	0.93[AMR][1000 genomes]
rs924073	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1048004	chr12:117170738-117219076	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv1039046	chr12:117170989-117225635	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117174000-117177000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:117174000-117177200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr12:117174200-117176800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr12:117174200-117176800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr12:117174200-117177200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr12:117174400-117177000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:117174400-117177000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:117174600-117176800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr12:117174600-117176800	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr12:117174600-117176800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:117174600-117176800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:117174600-117176800	Active TSS	Fetal Kidney	kidney
13	chr12:117174800-117176800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:117174800-117176800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:117174800-117177000	Active TSS	Brain Angular Gyrus	brain
16	chr12:117174800-117177200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:117175000-117176800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:117175000-117176800	Active TSS	Brain Anterior Caudate	brain
19	chr12:117175000-117176800	Active TSS	Brain Cingulate Gyrus	brain
20	chr12:117175000-117176800	Active TSS	NH-A	brain
21	chr12:117175000-117177000	Active TSS	NHLF	lung
22	chr12:117175400-117176800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:117176000-117176800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr12:117176000-117176800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr12:117176200-117176800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr12:117176200-117176800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr12:117176200-117176800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr12:117176200-117176800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:117176200-117176800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:117176200-117176800	Flanking Active TSS	Thymus	Thymus
31	chr12:117176200-117177000	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr12:117176200-117177000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr12:117176200-117177200	Flanking Active TSS	Dnd41	blood
34	chr12:117176400-117176800	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr12:117176400-117176800	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr12:117176400-117176800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:117176400-117176800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr12:117176400-117176800	Active TSS	Brain Germinal Matrix	brain
39	chr12:117176400-117176800	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr12:117176400-117177000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr12:117176400-117177000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr12:117176400-117177000	Flanking Active TSS	HepG2	liver
43	chr12:117176400-117177200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr12:117176400-117177200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr12:117176400-117177200	Enhancers	Spleen	Spleen
46	chr12:117176400-117177200	Flanking Active TSS	GM12878-XiMat	blood
47	chr12:117176400-117177200	Flanking Active TSS	Hela-S3	cervix
48	chr12:117176400-117179200	Weak transcription	Pancreas	Pancrea
49	chr12:117176600-117176800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:117176600-117176800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

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