Variant report

Variant	rs62257013
Chromosome Location	chr3:53384720-53384721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:107)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:107 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr3:53384698-53385054	K562	blood:	n/a	n/a
2	ARID3A	chr3:53384621-53384981	K562	blood:	n/a	n/a
3	SMC3	chr3:53384665-53385063	Hela-S3	cervix:	n/a	n/a
4	HDAC2	chr3:53384710-53385050	K562	blood:	n/a	n/a
5	CTCF	chr3:53384640-53384790	HCM	heart:	n/a	n/a
6	EP300	chr3:53384720-53384917	SK-N-SH_RA	brain:	n/a	n/a
7	RCOR1	chr3:53384719-53385009	Hela-S3	cervix:	n/a	n/a
8	TEAD4	chr3:53384478-53385154	K562	blood:	n/a	n/a
9	TRIM28	chr3:53384676-53384993	K562	blood:	n/a	n/a
10	CTCF	chr3:53384712-53384970	A549	lung:	n/a	n/a
11	GATA3	chr3:53384453-53385268	SK-N-SH	brain:	n/a	n/a
12	RAD21	chr3:53384666-53385066	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr3:53384621-53385159	HCT-116	colon:	n/a	n/a
14	RAD21	chr3:53384495-53385140	SK-N-SH	brain:	n/a	n/a
15	RAD21	chr3:53384559-53385159	HCT-116	colon:	n/a	n/a
16	POLR2A	chr3:53384699-53384957	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr3:53384627-53385097	K562	blood:	n/a	n/a
18	GATA3	chr3:53384649-53385008	MCF-7	breast:	n/a	n/a
19	GATA3	chr3:53384612-53385130	A549	lung:	n/a	n/a
20	CTCF	chr3:53384699-53385040	A549	lung:	n/a	n/a
21	POLR2A	chr3:53384509-53385089	HUVEC	blood vessel:	n/a	n/a
22	CTCF	chr3:53384700-53384850	A549	lung:	n/a	n/a
23	CTCF	chr3:53384720-53384870	BE2_C	brain:	n/a	n/a
24	RAD21	chr3:53384603-53385106	H1-hESC	embryonic stem cell:	n/a	n/a
25	PML	chr3:53384553-53385086	K562	blood:	n/a	n/a
26	TCF7L2	chr3:53384478-53385411	HEK293	kidney:	n/a	n/a
27	CTCF	chr3:53384718-53385061	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:53384719-53385012	K562	blood:	n/a	n/a
29	RAD21	chr3:53384710-53384996	GM12878	blood:	n/a	n/a
30	CTCF	chr3:53384720-53384870	GM12866	blood:	n/a	n/a
31	SPI1	chr3:53384650-53385063	HL-60	blood:	n/a	n/a
32	GATA1	chr3:53384692-53385041	PBDEFetal	blood:	n/a	n/a
33	CBX3	chr3:53384647-53385045	K562	blood:	n/a	n/a
34	CTCF	chr3:53384683-53385070	GM12878	blood:	n/a	n/a
35	GATA3	chr3:53384637-53385010	T-47D	breast:	n/a	n/a
36	TBL1XR1	chr3:53384598-53385080	K562	blood:	n/a	n/a
37	TEAD4	chr3:53384459-53385215	K562	blood:	n/a	n/a
38	RAD21	chr3:53384679-53385065	Hela-S3	cervix:	n/a	n/a
39	GATA3	chr3:53384414-53385283	A549	lung:	n/a	n/a
40	NR2F2	chr3:53384606-53385112	MCF-7	breast:	n/a	n/a
41	GATA3	chr3:53384453-53385211	MCF-7	breast:	n/a	n/a
42	NR2F2	chr3:53384481-53385130	K562	blood:	n/a	n/a
43	SMC3	chr3:53384710-53385046	GM12878	blood:	n/a	n/a
44	RAD21	chr3:53384623-53385141	A549	lung:	n/a	n/a
45	POLR2A	chr3:53384618-53385000	K562	blood:	n/a	n/a
46	CTCF	chr3:53384715-53385053	IMR90	lung:	n/a	n/a
47	CTCF	chr3:53384680-53384830	HFF-Myc	foreskin:	n/a	n/a
48	RCOR1	chr3:53384621-53385096	K562	blood:	n/a	n/a
49	ZMIZ1	chr3:53384673-53385195	K562	blood:	n/a	n/a
50	RAD21	chr3:53384686-53384964	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:53379818..53382872-chr3:53383251..53384852,3	K562	blood:
2	chr3:53380268..53383012-chr3:53383580..53385779,3	MCF-7	breast:
3	chr3:53381477..53383180-chr3:53384044..53385998,2	MCF-7	breast:
4	chr3:53380422..53382928-chr3:53383567..53386343,3	K562	blood:

No data

Variant related genes	Relation type
DCP1A	TF binding region
ENSG00000162290	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10433617	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10433618	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1108506	0.94[EUR][1000 genomes]
rs11551405	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17030933	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17030934	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17234771	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17235667	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56654807	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58558806	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59145995	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62252819	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62255989	0.83[AMR][1000 genomes]
rs62255993	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62255994	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62255999	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256000	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62256003	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62256009	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256043	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256049	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256050	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256053	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256962	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62256964	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256965	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256966	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256968	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256969	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257004	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257007	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257009	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257024	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780100	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805246	1.00[ASN][1000 genomes]
rs73080266	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73080271	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73080273	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73080295	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73082274	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7622159	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9830594	0.89[EUR][1000 genomes]
rs9830895	0.91[EUR][1000 genomes]
rs9846315	0.93[EUR][1000 genomes]
rs9850440	0.91[EUR][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	nsv876801	chr3:53325905-53467506	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv876802	chr3:53325905-53470863	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53382400-53384800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:53382400-53385000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:53382400-53388600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:53382400-53388600	Weak transcription	NH-A	brain
5	chr3:53382600-53389000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:53383800-53385400	Enhancers	Primary hematopoietic stem cells	blood
7	chr3:53383800-53385600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:53384000-53387800	Enhancers	HUVEC	blood vessel
9	chr3:53384200-53385600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:53384400-53385000	Enhancers	Duodenum Mucosa	Duodenum
11	chr3:53384400-53385200	Enhancers	Osteobl	bone
12	chr3:53384400-53385400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:53384400-53385400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:53384400-53385400	Enhancers	Fetal Intestine Large	intestine
15	chr3:53384400-53385400	Enhancers	Fetal Intestine Small	intestine
16	chr3:53384400-53385400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr3:53384400-53385400	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr3:53384400-53385600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:53384400-53385600	Enhancers	Hela-S3	cervix
20	chr3:53384400-53385600	Enhancers	K562	blood
21	chr3:53384600-53385000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:53384600-53385000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr3:53384600-53385200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr3:53384600-53385200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:53384600-53385200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:53384600-53385200	Enhancers	Adipose Nuclei	Adipose
27	chr3:53384600-53385200	Flanking Active TSS	A549	lung
28	chr3:53384600-53385400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:53384600-53385400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:53384600-53385400	Enhancers	Fetal Lung	lung
31	chr3:53384600-53385400	Enhancers	Placenta	Placenta
32	chr3:53384600-53385400	Enhancers	HepG2	liver
33	chr3:53384600-53385400	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links