Variant report

Variant	rs1533373
Chromosome Location	chr1:84971041-84971042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:164)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:164 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr1:84970873-84971303	HepG2	liver:	n/a	n/a
2	JUN	chr1:84970079-84973077	K562	blood:	n/a	chr1:84970176-84970185 chr1:84972305-84972317 chr1:84972307-84972316
3	ARID3A	chr1:84970808-84971465	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:84969985-84972746	HCT-116	colon:	n/a	n/a
5	MXI1	chr1:84970410-84973047	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:84970990-84972853	K562	blood:	n/a	n/a
7	POLR2A	chr1:84970863-84972828	GM18526	blood:	n/a	n/a
8	MYC	chr1:84970758-84971361	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:84970808-84971620	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:84970891-84972710	PFSK-1	brain:	n/a	n/a
11	MAX	chr1:84970764-84972587	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:84970344-84972750	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:84970407-84973119	GM19099	blood:	n/a	n/a
14	CHD1	chr1:84971004-84971438	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:84970141-84972678	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:84970931-84972928	K562	blood:	n/a	n/a
17	TEAD4	chr1:84970725-84971356	HepG2	liver:	n/a	n/a
18	EP300	chr1:84970833-84971399	HepG2	liver:	n/a	chr1:84971155-84971169
19	CHD2	chr1:84970985-84972836	GM12878	blood:	n/a	n/a
20	BHLHE40	chr1:84970957-84972805	GM12878	blood:	n/a	chr1:84971560-84971576
21	POLR2A	chr1:84970276-84972805	Hela-S3	cervix:	n/a	n/a
22	PML	chr1:84970167-84973030	GM12878	blood:	n/a	n/a
23	SMC3	chr1:84970269-84972875	Hela-S3	cervix:	n/a	chr1:84972211-84972219
24	POLR2A	chr1:84970756-84971058	MCF-7	breast:	n/a	n/a
25	TBP	chr1:84970234-84971496	Hela-S3	cervix:	n/a	n/a
26	NFATC1	chr1:84970321-84971066	GM12878	blood:	n/a	n/a
27	RCOR1	chr1:84970161-84972710	Hela-S3	cervix:	n/a	n/a
28	MXI1	chr1:84969756-84973236	IMR90	lung:	n/a	n/a
29	POLR2A	chr1:84957385-84973725	K562	blood:	n/a	n/a
30	HEY1	chr1:84970857-84972714	K562	blood:	n/a	n/a
31	CEBPB	chr1:84970994-84971455	K562	blood:	n/a	chr1:84971158-84971169 chr1:84971157-84971168 chr1:84971157-84971168 chr1:84971157-84971170 chr1:84971157-84971170
32	MAX	chr1:84970957-84972860	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:84970922-84972590	HepG2	liver:	n/a	n/a
34	RXRA	chr1:84970883-84971232	HepG2	liver:	n/a	chr1:84971028-84971037
35	RELA	chr1:84970322-84972863	GM18505	blood:	n/a	n/a
36	TEAD4	chr1:84970869-84972817	K562	blood:	n/a	n/a
37	RAD21	chr1:84970942-84972637	IMR90	lung:	n/a	n/a
38	CEBPB	chr1:84970970-84971499	IMR90	lung:	n/a	chr1:84971158-84971169 chr1:84971157-84971168 chr1:84971157-84971168 chr1:84971157-84971170 chr1:84971157-84971170
39	EBF1	chr1:84970370-84971572	GM12878	blood:	n/a	chr1:84970547-84970558
40	MYC	chr1:84970825-84972868	K562	blood:	n/a	n/a
41	HDAC2	chr1:84970909-84971218	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:84970975-84971130	HepG2	liver:	n/a	n/a
43	TCF7L2	chr1:84970999-84971614	Hela-S3	cervix:	n/a	n/a
44	GTF2F1	chr1:84970873-84971580	Hela-S3	cervix:	n/a	n/a
45	TBL1XR1	chr1:84970903-84972867	K562	blood:	n/a	n/a
46	CEBPB	chr1:84970957-84971407	ECC-1	luminal epithelium:	n/a	chr1:84971158-84971169 chr1:84971157-84971168 chr1:84971157-84971168 chr1:84971157-84971170 chr1:84971157-84971170
47	NFIC	chr1:84970858-84971258	HepG2	liver:	n/a	n/a
48	MAX	chr1:84970795-84972663	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:84970933-84971160	ECC-1	luminal epithelium:	n/a	n/a
50	MYC	chr1:84970667-84972814	NB4	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:84971011-84971061	HUVEC	blood vessel:	n/a
2	chr1:84971011-84971061	GM12892	blood:	n/a
3	chr1:84971011-84971061	HMEC	breast:	n/a
4	chr1:84971011-84971061	HCF	heart:	n/a
5	chr1:84971011-84971061	AG10803	skin:	n/a
6	chr1:84971011-84971061	U87	brain:	n/a
7	chr1:84971011-84971061	HCM	heart:	n/a
8	chr1:84971011-84971061	H1-hESC	embryonic stem cell:	embryo
9	chr1:84971011-84971061	HIPEpiC	eye:	n/a
10	chr1:84971011-84971061	BE2_C	brain:	n/a
11	chr1:84971011-84971061	HAEpiC	amniotic membrane:	n/a
12	chr1:84971011-84971061	SK-N-SH_RA	brain:	n/a
13	chr1:84971011-84971061	BJ	skin:	n/a
14	chr1:84971011-84971061	HL-60	blood:	n/a
15	chr1:84971011-84971061	Hepatocyte	liver:	n/a
16	chr1:84971011-84971061	NB4	blood:	n/a
17	chr1:84971011-84971061	NH-A	brain:	n/a
18	chr1:84971011-84971061	HCT-116	colon:	n/a
19	chr1:84971011-84971061	GM12878	blood:	n/a
20	chr1:84971011-84971061	Caco-2	colon:	n/a
21	chr1:84971011-84971061	HEK293	kidney:	embryo
22	chr1:84971011-84971061	A549	lung:	n/a
23	chr1:84971011-84971061	CMK	blood:	n/a
24	chr1:84971011-84971061	HCPEpiC	choroid plexus:	n/a
25	chr1:84971011-84971061	IMR90	lung:	fetal
26	chr1:84971011-84971061	GM12891	blood:	n/a
27	chr1:84971011-84971061	ProgFib	skin:	n/a
28	chr1:84971011-84971061	SKMC	muscle:	n/a
29	chr1:84971011-84971061	HEEpiC	esophagus:	n/a
30	chr1:84971011-84971061	AG04449	skin:	fetal
31	chr1:84971011-84971061	NT2-D1	testis:	n/a
32	chr1:84971011-84971061	HepG2	liver:	n/a
33	chr1:84971011-84971061	ovcar-3	ovarian:	n/a
34	chr1:84971011-84971061	AG09309	skin:	n/a
35	chr1:84971011-84971061	HRCEpiC	kidney:	n/a
36	chr1:84971011-84971061	AG09319	gingival:	n/a
37	chr1:84971011-84971061	PANC-1	pancreas:	n/a
38	chr1:84971011-84971061	Jurkat	blood:	n/a
39	chr1:84971011-84971061	K562	blood:	n/a
40	chr1:84971011-84971061	MCF-7	breast:	n/a
41	chr1:84971011-84971061	RPTEC	kidney:	n/a
42	chr1:84971011-84971061	NHBE	bronchial:	n/a
43	chr1:84971011-84971061	MCF10A-Er-Src	breast:	n/a
44	chr1:84971011-84971061	PrEC	prostate:	n/a
45	chr1:84971011-84971061	ECC-1	luminal epithelium:	n/a
46	chr1:84971011-84971061	SAEC	small airway:	n/a
47	chr1:84971011-84971061	Hela-S3	cervix:	n/a
48	chr1:84971011-84971061	T-47D	breast:	n/a
49	chr1:84971011-84971061	SK-N-MC	brain:	n/a
50	chr1:84971011-84971061	SK-N-SH	brain:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:84943777..84946552-chr1:84970497..84973179,2	MCF-7	breast:
2	chr1:84944684..84947410-chr1:84970225..84973395,6	MCF-7	breast:
3	chr1:84971039..84971904-chr9:130565441..130566038,2	Hela-S3	cervix:
4	chr1:84969735..84979623-chr1:84983174..84994888,16	K562	blood:
5	chr1:84970952..84971562-chrX:101186456..101187129,2	Hela-S3	cervix:
6	chr1:84970994..84971901-chr10:75570657..75571609,2	Hela-S3	cervix:
7	chr1:84543103..84544767-chr1:84969541..84972530,2	K562	blood:
8	chr1:84969596..84972494-chr1:85154864..85156849,3	K562	blood:
9	chr1:84970994..84973830-chr1:85154472..85157447,5	K562	blood:
10	chr1:84966614..84978118-chr1:85034515..85041986,38	K562	blood:
11	chr1:84966967..84974535-chr1:85036439..85041823,24	K562	blood:
12	chr1:84970551..84971520-chr5:151151462..151152365,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
SPATA1	TF binding region
GNG5	TF binding region
GNG5	CpG island
SPATA1	CpG island
ENSG00000117155	Chromatin interaction
ENSG00000272916	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000136877	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000166432	Chromatin interaction
ENSG00000271576	Chromatin interaction
ENSG00000145907	Chromatin interaction
ENSG00000117133	Chromatin interaction
ENSG00000166507	Chromatin interaction
ENSG00000142875	Chromatin interaction
ENSG00000177556	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10082140	1.00[EUR][1000 genomes]
rs10082196	1.00[EUR][1000 genomes]
rs10874447	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10874448	0.82[AFR][1000 genomes]
rs11164008	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808831	1.00[EUR][1000 genomes]
rs12057445	1.00[EUR][1000 genomes]
rs12063628	1.00[EUR][1000 genomes]
rs12063669	1.00[EUR][1000 genomes]
rs1340522	1.00[EUR][1000 genomes]
rs1515142	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17131643	1.00[EUR][1000 genomes]
rs172736	1.00[EUR][1000 genomes]
rs2911584	1.00[AMR][1000 genomes]
rs2911608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2943665	1.00[AMR][1000 genomes]
rs2994924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2994925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs312398	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6671641	1.00[EUR][1000 genomes]
rs72943947	1.00[EUR][1000 genomes]
rs7413066	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7529017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7533636	1.00[EUR][1000 genomes]
rs7546355	1.00[EUR][1000 genomes]
rs784834	1.00[EUR][1000 genomes]
rs9804106	1.00[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	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84968600-84971400	Active TSS	Right Atrium	heart
2	chr1:84968800-84973200	Active TSS	Right Ventricle	heart
3	chr1:84969000-84973000	Active TSS	Left Ventricle	heart
4	chr1:84969200-84973200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:84969400-84971200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr1:84969400-84971400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:84969400-84973200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:84969600-84971200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:84969800-84973000	Active TSS	Muscle Satellite Cultured Cells	--
10	chr1:84969800-84973000	Active TSS	Aorta	Aorta
11	chr1:84969800-84973000	Active TSS	HSMM	muscle
12	chr1:84970000-84971200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr1:84970000-84971200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:84970000-84972800	Active TSS	Ovary	ovary
15	chr1:84970000-84973000	Active TSS	Stomach Smooth Muscle	stomach
16	chr1:84970000-84973200	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr1:84970000-84973200	Active TSS	Fetal Intestine Large	intestine
18	chr1:84970000-84973600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:84970000-84973600	Active TSS	GM12878-XiMat	blood
20	chr1:84970000-84973600	Active TSS	NHLF	lung
21	chr1:84970200-84971200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
22	chr1:84970200-84971200	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr1:84970200-84971200	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr1:84970200-84972800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:84970200-84972800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:84970200-84973000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:84970200-84973000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:84970200-84973000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:84970200-84973000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:84970200-84973000	Active TSS	Fetal Muscle Trunk	muscle
31	chr1:84970200-84973000	Active TSS	HSMMtube	muscle
32	chr1:84970200-84973000	Active TSS	NH-A	brain
33	chr1:84970200-84973200	Active TSS	Psoas Muscle	Psoas
34	chr1:84970200-84973200	Active TSS	NHDF-Ad	bronchial
35	chr1:84970200-84973400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:84970200-84973400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:84970400-84971200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
38	chr1:84970400-84971200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr1:84970400-84971200	Active TSS	HepG2	liver
40	chr1:84970400-84971400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr1:84970400-84971400	Flanking Active TSS	Fetal Brain Male	brain
42	chr1:84970400-84972600	Active TSS	Small Intestine	intestine
43	chr1:84970400-84972800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:84970400-84972800	Active TSS	Osteobl	bone
45	chr1:84970400-84973000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr1:84970400-84973000	Active TSS	H9 Cell Line	embryonic stem cell
47	chr1:84970400-84973000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:84970400-84973000	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr1:84970400-84973000	Active TSS	Fetal Intestine Small	intestine
50	chr1:84970400-84973000	Active TSS	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links