Variant report

Variant	rs35989686
Chromosome Location	chr12:122062593-122062594
allele	A/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	CTCF	chr12:122062562-122062889	H1-hESC	embryonic stem cell:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
2	MXI1	chr12:122062542-122063106	SK-N-SH	brain:	n/a	n/a
3	USF1	chr12:122062593-122062886	SK-N-SH_RA	brain:	n/a	chr12:122062726-122062737
4	PBX3	chr12:122062584-122063014	SK-N-SH	brain:	n/a	n/a
5	RAD21	chr12:122062561-122062856	A549	lung:	n/a	chr12:122062674-122062693 chr12:122062680-122062689 chr12:122062684-122062691
6	CTCF	chr12:122062580-122062730	HAc	cerebellar:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
7	ZNF143	chr12:122062564-122062845	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr12:122062580-122062730	WI-38	lung:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
9	CREB1	chr12:122062506-122062951	H1-hESC	embryonic stem cell:	n/a	n/a
10	SMC3	chr12:122062501-122063005	GM12878	blood:	n/a	chr12:122062678-122062692
11	FOXA1	chr12:122062577-122062840	T-47D	breast:	n/a	n/a
12	CTCF	chr12:122062567-122062841	GM12892	blood:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
13	CTCF	chr12:122062590-122062788	HepG2	liver:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
14	CTCF	chr12:122062575-122062828	LNCaP	prostate:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
15	BCLAF1	chr12:122062576-122062927	GM12878	blood:	n/a	n/a
16	CTCF	chr12:122062587-122062825	Fibrobl	skin:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
17	CTCF	chr12:122062547-122062906	A549	lung:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
18	CTCF	chr12:122062580-122062730	HFF-Myc	foreskin:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
19	CBX3	chr12:122062573-122062862	K562	blood:	n/a	n/a
20	MAX	chr12:122062570-122062909	K562	blood:	n/a	n/a
21	MAX	chr12:122062563-122063131	K562	blood:	n/a	n/a
22	ZNF143	chr12:122062512-122062855	GM12878	blood:	n/a	n/a
23	RAD21	chr12:122062552-122062811	GM12878	blood:	n/a	chr12:122062674-122062693 chr12:122062680-122062689 chr12:122062684-122062691
24	CTCF	chr12:122062564-122062842	GM19238	blood:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
25	CTCF	chr12:122062580-122062730	HFF	foreskin:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
26	USF1	chr12:122062581-122062945	SK-N-SH_RA	brain:	n/a	chr12:122062726-122062737
27	CTCF	chr12:122062593-122062801	GM20000	blood:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
28	YY1	chr12:122062579-122062769	HepG2	liver:	n/a	n/a
29	MAX	chr12:122062524-122062997	A549	lung:	n/a	n/a
30	RAD21	chr12:122062496-122062949	H1-hESC	embryonic stem cell:	n/a	chr12:122062674-122062693 chr12:122062680-122062689 chr12:122062684-122062691
31	YY1	chr12:122062588-122062909	H1-hESC	embryonic stem cell:	n/a	n/a
32	RAD21	chr12:122062568-122062881	H1-hESC	embryonic stem cell:	n/a	chr12:122062674-122062693 chr12:122062680-122062689 chr12:122062684-122062691
33	ZNF384	chr12:122062529-122062890	GM12878	blood:	n/a	n/a
34	CTCF	chr12:122062520-122063227	A549	lung:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
35	RAD21	chr12:122062517-122062850	HepG2	liver:	n/a	chr12:122062674-122062693 chr12:122062680-122062689 chr12:122062684-122062691
36	CTCF	chr12:122062591-122062812	LNCaP	prostate:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
37	GABPA	chr12:122062592-122062785	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAX	chr12:122062581-122062863	K562	blood:	n/a	n/a
39	USF1	chr12:122062566-122063006	A549	lung:	n/a	chr12:122062726-122062737
40	RAD21	chr12:122062558-122062942	ECC-1	luminal epithelium:	n/a	chr12:122062674-122062693 chr12:122062680-122062689 chr12:122062684-122062691
41	CTCF	chr12:122062520-122062833	H1-hESC	embryonic stem cell:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
42	E2F6	chr12:122062565-122063026	A549	lung:	n/a	chr12:122062673-122062687 chr12:122062672-122062681
43	USF1	chr12:122062590-122062856	A549	lung:	n/a	chr12:122062726-122062737
44	MYC	chr12:122062540-122063309	A549	lung:	n/a	n/a
45	CTCF	chr12:122062575-122062827	ECC-1	luminal epithelium:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
46	BHLHE40	chr12:122062580-122062902	GM12878	blood:	n/a	n/a
47	CTCF	chr12:122062559-122062827	GM19240	blood:	n/a	chr12:122062678-122062691 chr12:122062681-122062689 chr12:122062676-122062694 chr12:122062671-122062692 chr12:122062678-122062691 chr12:122062677-122062693
48	TCF12	chr12:122062474-122063104	A549	lung:	n/a	n/a
49	E2F4	chr12:122062562-122062859	MCF10A-Er-Src	breast:	n/a	chr12:122062673-122062687 chr12:122062672-122062681
50	MXI1	chr12:122062581-122062917	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121990248..121991227-chr12:122062191..122062820,7	MCF-7	breast:
2	chr12:122011020..122013695-chr12:122061585..122064129,2	K562	blood:
3	chr12:122014421..122021664-chr12:122061311..122067896,12	MCF-7	breast:
4	chr12:121971488..121973015-chr12:122062542..122064592,2	K562	blood:
5	chr12:122015964..122018942-chr12:122062430..122066173,5	K562	blood:
6	chr12:121990007..121990815-chr12:122062235..122063163,4	K562	blood:
7	chr12:122015992..122019375-chr12:122062452..122065791,4	MCF-7	breast:
8	chr12:122057244..122059003-chr12:122062084..122064323,2	K562	blood:

Variant related genes	Relation type
ORAI1	TF binding region
ENSG00000256742	Chromatin interaction
ENSG00000089094	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10770190	0.82[EUR][1000 genomes]
rs1113409	0.87[ASN][1000 genomes]
rs11502393	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11610515	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12300327	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12308869	0.87[ASN][1000 genomes]
rs12313273	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12319775	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3741595	0.89[ASN][1000 genomes]
rs4760125	0.86[ASN][1000 genomes]
rs59988934	0.83[EUR][1000 genomes]
rs6486776	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6486787	0.83[EUR][1000 genomes]
rs7313601	0.82[EUR][1000 genomes]
rs73227920	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73227933	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7398511	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122028800-122064000	Weak transcription	Right Atrium	heart
2	chr12:122048800-122062800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:122048800-122062800	Weak transcription	Fetal Intestine Small	intestine
4	chr12:122049400-122062800	Weak transcription	Thymus	Thymus
5	chr12:122049800-122062600	Weak transcription	Hela-S3	cervix
6	chr12:122050000-122063800	Weak transcription	Fetal Stomach	stomach
7	chr12:122050200-122062800	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:122053000-122062800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:122057000-122062600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:122057200-122062600	Weak transcription	GM12878-XiMat	blood
11	chr12:122057800-122062600	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:122058000-122062600	Weak transcription	Osteobl	bone
13	chr12:122058000-122062800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:122058000-122062800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:122058000-122062800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:122058000-122062800	Weak transcription	A549	lung
17	chr12:122058000-122062800	Weak transcription	HSMM	muscle
18	chr12:122058200-122062800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:122058200-122062800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:122058400-122062600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:122058400-122062600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr12:122058400-122062600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:122058400-122062800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:122058400-122062800	Weak transcription	Primary T cells from cord blood	blood
25	chr12:122058400-122062800	Weak transcription	NH-A	brain
26	chr12:122058400-122064000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:122058600-122062600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:122058600-122062600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:122058600-122062600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:122058600-122062600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:122058600-122062600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:122058600-122062600	Weak transcription	HUVEC	blood vessel
33	chr12:122058600-122062800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:122058600-122062800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:122058600-122062800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:122058600-122062800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:122058600-122062800	Weak transcription	Primary B cells from cord blood	blood
38	chr12:122058600-122062800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:122058600-122062800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr12:122058800-122062600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr12:122058800-122062600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:122058800-122062600	Weak transcription	HepG2	liver
43	chr12:122058800-122062600	Weak transcription	K562	blood
44	chr12:122058800-122062600	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr12:122058800-122062800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:122058800-122062800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:122058800-122062800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:122058800-122062800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:122058800-122062800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:122061200-122064000	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links