Variant report

Variant	rs3809324
Chromosome Location	chr12:48399028-48399029
allele	A/C
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	MAX	chr12:48397501-48399134	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZBTB7A	chr12:48397887-48399036	ECC-1	luminal epithelium:	n/a	n/a
3	CHD2	chr12:48398813-48399091	HepG2	liver:	n/a	n/a
4	ZNF143	chr12:48398697-48399334	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3A	chr12:48397330-48399218	H1-hESC	embryonic stem cell:	n/a	chr12:48397945-48397958
6	TCF12	chr12:48397839-48399260	ECC-1	luminal epithelium:	n/a	chr12:48398407-48398414
7	E2F6	chr12:48397408-48399034	H1-hESC	embryonic stem cell:	n/a	chr12:48398447-48398459 chr12:48398371-48398380
8	ZBTB7A	chr12:48397763-48399149	ECC-1	luminal epithelium:	n/a	n/a
9	SP1	chr12:48398357-48399178	H1-hESC	embryonic stem cell:	n/a	chr12:48398899-48398908 chr12:48399020-48399034 chr12:48398670-48398684 chr12:48398449-48398463 chr12:48398575-48398587 chr12:48398576-48398585 chr12:48398575-48398587 chr12:48398487-48398496 chr12:48398577-48398586 chr12:48398897-48398909 chr12:48398371-48398380 chr12:48398897-48398909 chr12:48398898-48398912 chr12:48398898-48398908 chr12:48398607-48398616
10	CHD2	chr12:48398545-48399082	H1-hESC	embryonic stem cell:	n/a	n/a
11	TBP	chr12:48397641-48399143	H1-hESC	embryonic stem cell:	n/a	n/a
12	SUZ12	chr12:48396473-48400031	NT2-D1	testis:	n/a	n/a
13	CTBP2	chr12:48397798-48399716	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48392370..48394722-chr12:48397446..48401400,3	K562	blood:
2	chr12:48392370..48394865-chr12:48396464..48400282,3	K562	blood:

Variant related genes	Relation type
COL2A1	TF binding region
ENSG00000139219	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10875714	0.88[EUR][1000 genomes]
rs10875715	0.86[EUR][1000 genomes]
rs12228854	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12308909	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1990028	0.84[AMR][1000 genomes]
rs2213163	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2898056	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3737548	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3782915	0.88[EUR][1000 genomes]
rs3809322	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56037230	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56959315	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs740022	0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3809324	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs3809324	RP1-228P16.1	cis	Artery Tibial	GTEx
rs3809324	RP1-228P16.1	cis	Thyroid	GTEx
rs3809324	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs3809324	ZNF641	cis	Muscle Skeletal	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48394800-48399200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
2	chr12:48395000-48399200	Bivalent Enhancer	Fetal Thymus	thymus
3	chr12:48395800-48399200	Bivalent/Poised TSS	Fetal Kidney	kidney
4	chr12:48397000-48399200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:48397200-48399200	Bivalent Enhancer	Fetal Brain Male	brain
6	chr12:48397400-48399200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
7	chr12:48397400-48399400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:48397600-48399400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:48397800-48399200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:48397800-48399600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr12:48397800-48399800	Bivalent Enhancer	Fetal Lung	lung
12	chr12:48398000-48399200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
13	chr12:48398000-48399200	Bivalent Enhancer	Fetal Heart	heart
14	chr12:48398000-48399400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
15	chr12:48398200-48399200	Bivalent Enhancer	Primary B cells from cord blood	blood
16	chr12:48398200-48399200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
17	chr12:48398200-48399400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
18	chr12:48398400-48399200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
19	chr12:48398400-48399200	Bivalent Enhancer	Brain Anterior Caudate	brain
20	chr12:48398400-48399200	Bivalent Enhancer	Lung	lung
21	chr12:48398600-48399200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:48398600-48399200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:48398600-48399200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:48398600-48399200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
25	chr12:48398600-48399200	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
26	chr12:48398600-48399200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
27	chr12:48398600-48399200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:48398600-48399200	Bivalent Enhancer	Ovary	ovary
29	chr12:48398600-48399200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
30	chr12:48398600-48399400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:48398600-48399400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:48398600-48399400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:48398600-48399400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
34	chr12:48398600-48399600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
35	chr12:48398600-48399600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
36	chr12:48398600-48399600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:48398800-48399200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
38	chr12:48398800-48399200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:48398800-48399200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:48398800-48399200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
41	chr12:48398800-48399200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:48398800-48399200	Bivalent Enhancer	Brain Hippocampus Middle	brain
43	chr12:48398800-48399200	Bivalent Enhancer	Brain Substantia Nigra	brain
44	chr12:48398800-48399200	Bivalent Enhancer	Fetal Intestine Large	intestine
45	chr12:48398800-48399400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:48398800-48399400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
47	chr12:48398800-48399400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr12:48398800-48399400	Bivalent Enhancer	Fetal Muscle Leg	muscle
49	chr12:48398800-48399400	Bivalent Enhancer	Fetal Stomach	stomach
50	chr12:48398800-48399400	Strong transcription	Right Atrium	heart

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