Variant report

Variant	rs12317373
Chromosome Location	chr12:48399230-48399231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr12:48398697-48399334	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF12	chr12:48397839-48399260	ECC-1	luminal epithelium:	n/a	chr12:48398407-48398414
3	SUZ12	chr12:48396473-48400031	NT2-D1	testis:	n/a	n/a
4	CTBP2	chr12:48397798-48399716	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:48399180-48399230	MCF-7	breast:	n/a
2	chr12:48399180-48399230	AG09319	gingival:	n/a
3	chr12:48399180-48399230	HUVEC	blood vessel:	n/a
4	chr12:48399180-48399230	K562	blood:	n/a
5	chr12:48399180-48399230	HEEpiC	esophagus:	n/a
6	chr12:48399180-48399230	HNPCEpiC	eye:	n/a
7	chr12:48399180-48399230	AG04450	lung:	fetal
8	chr12:48399180-48399230	HRPEpiC	eye:	n/a
9	chr12:48399180-48399230	NHBE	bronchial:	n/a
10	chr12:48399180-48399230	IMR90	lung:	fetal
11	chr12:48399180-48399230	GM12878	blood:	n/a
12	chr12:48399180-48399230	HAEpiC	amniotic membrane:	n/a
13	chr12:48399180-48399230	A549	lung:	n/a
14	chr12:48399180-48399230	HRE	kidney:	n/a
15	chr12:48399180-48399230	HEK293	kidney:	embryo
16	chr12:48399180-48399230	HCT-116	colon:	n/a
17	chr12:48399180-48399230	BE2_C	brain:	n/a
18	chr12:48399180-48399230	HCM	heart:	n/a
19	chr12:48399180-48399230	NHDF-neo	bronchial:	n/a
20	chr12:48399180-48399230	MCF10A-Er-Src	breast:	n/a
21	chr12:48399180-48399230	NH-A	brain:	n/a
22	chr12:48399180-48399230	LNCaP	prostate:	n/a
23	chr12:48399180-48399230	HIPEpiC	eye:	n/a
24	chr12:48399180-48399230	ECC-1	luminal epithelium:	n/a
25	chr12:48399180-48399230	HCPEpiC	choroid plexus:	n/a
26	chr12:48399180-48399230	T-47D	breast:	n/a
27	chr12:48399180-48399230	GM06990	blood:	n/a
28	chr12:48399180-48399230	Jurkat	blood:	n/a
29	chr12:48399180-48399230	SAEC	small airway:	n/a
30	chr12:48399180-48399230	SK-N-SH	brain:	n/a
31	chr12:48399180-48399230	HCF	heart:	n/a
32	chr12:48399180-48399230	PANC-1	pancreas:	n/a
33	chr12:48399180-48399230	NB4	blood:	n/a
34	chr12:48399180-48399230	SK-N-MC	brain:	n/a
35	chr12:48399180-48399230	AG09309	skin:	n/a
36	chr12:48399180-48399230	Hela-S3	cervix:	n/a
37	chr12:48399180-48399230	GM12892	blood:	n/a
38	chr12:48399180-48399230	PFSK-1	brain:	n/a
39	chr12:48399180-48399230	HL-60	blood:	n/a
40	chr12:48399180-48399230	NT2-D1	testis:	n/a
41	chr12:48399180-48399230	HMEC	breast:	n/a
42	chr12:48399180-48399230	PrEC	prostate:	n/a
43	chr12:48399180-48399230	HepG2	liver:	n/a
44	chr12:48399180-48399230	RPTEC	kidney:	n/a
45	chr12:48399180-48399230	Caco-2	colon:	n/a
46	chr12:48399180-48399230	BJ	skin:	n/a
47	chr12:48399180-48399230	Hepatocyte	liver:	n/a
48	chr12:48399180-48399230	AG10803	skin:	n/a
49	chr12:48399180-48399230	SKMC	muscle:	n/a
50	chr12:48399180-48399230	AG04449	skin:	fetal

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48392370..48394722-chr12:48397446..48401400,3	K562	blood:
2	chr12:48399203..48400811-chr12:48412734..48415114,2	K562	blood:
3	chr12:48392370..48394865-chr12:48396464..48400282,3	K562	blood:
4	chr12:48399203..48401006-chr12:48440249..48442960,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL2A1-1	chr12:48399060-48399286	ENSG00000258203

No data

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

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10160938	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168280	1.00[AMR][1000 genomes]
rs11168352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12308796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74085274	1.00[AMR][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

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48397400-48399400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:48397600-48399400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:48397800-48399600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr12:48397800-48399800	Bivalent Enhancer	Fetal Lung	lung
5	chr12:48398000-48399400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr12:48398200-48399400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr12:48398600-48399400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:48398600-48399400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48398600-48399400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:48398600-48399400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
11	chr12:48398600-48399600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr12:48398600-48399600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
13	chr12:48398600-48399600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:48398800-48399400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:48398800-48399400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
16	chr12:48398800-48399400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr12:48398800-48399400	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr12:48398800-48399400	Bivalent Enhancer	Fetal Stomach	stomach
19	chr12:48398800-48399400	Strong transcription	Right Atrium	heart
20	chr12:48398800-48399400	Flanking Bivalent TSS/Enh	HepG2	liver
21	chr12:48398800-48399600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr12:48399000-48399400	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:48399000-48399400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:48399000-48399400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr12:48399000-48399400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
26	chr12:48399000-48399800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
27	chr12:48399000-48400200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:48399200-48399400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:48399200-48399400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
30	chr12:48399200-48399400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
31	chr12:48399200-48399600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
32	chr12:48399200-48399600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:48399200-48400000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:48399200-48400200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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