Variant report

Variant	rs57747253
Chromosome Location	chr3:23247318-23247319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr3:23247211-23247411	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:23247317-23247367	AG04450	lung:	fetal
2	chr3:23247317-23247367	MCF10A-Er-Src	breast:	n/a
3	chr3:23247317-23247367	PrEC	prostate:	n/a
4	chr3:23247317-23247367	NHBE	bronchial:	n/a
5	chr3:23247317-23247367	HCT-116	colon:	n/a
6	chr3:23247317-23247367	GM19239	blood:	n/a
7	chr3:23247317-23247367	HEEpiC	esophagus:	n/a
8	chr3:23247317-23247367	MCF-7	breast:	n/a
9	chr3:23247317-23247367	T-47D	breast:	n/a
10	chr3:23247317-23247367	AG09319	gingival:	n/a
11	chr3:23247317-23247367	ECC-1	luminal epithelium:	n/a
12	chr3:23247317-23247367	U87	brain:	n/a
13	chr3:23247317-23247367	HCPEpiC	choroid plexus:	n/a
14	chr3:23247317-23247367	BE2_C	brain:	n/a
15	chr3:23247317-23247367	HRPEpiC	eye:	n/a
16	chr3:23247317-23247367	PANC-1	pancreas:	n/a
17	chr3:23247317-23247367	HNPCEpiC	eye:	n/a
18	chr3:23247317-23247367	H1-hESC	embryonic stem cell:	embryo
19	chr3:23247317-23247367	LNCaP	prostate:	n/a
20	chr3:23247317-23247367	HCF	heart:	n/a
21	chr3:23247317-23247367	NH-A	brain:	n/a
22	chr3:23247317-23247367	HL-60	blood:	n/a
23	chr3:23247317-23247367	NHDF-neo	bronchial:	n/a
24	chr3:23247317-23247367	HEK293	kidney:	embryo
25	chr3:23247317-23247367	HAEpiC	amniotic membrane:	n/a
26	chr3:23247317-23247367	HCM	heart:	n/a
27	chr3:23247317-23247367	BJ	skin:	n/a
28	chr3:23247317-23247367	GM12878	blood:	n/a
29	chr3:23247317-23247367	SK-N-MC	brain:	n/a
30	chr3:23247317-23247367	SK-N-SH_RA	brain:	n/a
31	chr3:23247317-23247367	HRCEpiC	kidney:	n/a
32	chr3:23247317-23247367	NT2-D1	testis:	n/a
33	chr3:23247317-23247367	A549	lung:	n/a
34	chr3:23247317-23247367	ProgFib	skin:	n/a
35	chr3:23247317-23247367	SAEC	small airway:	n/a
36	chr3:23247317-23247367	AG04449	skin:	fetal
37	chr3:23247317-23247367	SK-N-SH	brain:	n/a
38	chr3:23247317-23247367	HPAEpiC	pulmonary alveolar:	n/a
39	chr3:23247317-23247367	Caco-2	colon:	n/a
40	chr3:23247317-23247367	AoSMC	blood vessel:	n/a
41	chr3:23247317-23247367	HUVEC	blood vessel:	n/a
42	chr3:23247317-23247367	ovcar-3	ovarian:	n/a
43	chr3:23247317-23247367	Hela-S3	cervix:	n/a
44	chr3:23247317-23247367	NB4	blood:	n/a
45	chr3:23247317-23247367	Hepatocyte	liver:	n/a
46	chr3:23247317-23247367	AG09309	skin:	n/a
47	chr3:23247317-23247367	GM12891	blood:	n/a
48	chr3:23247317-23247367	HIPEpiC	eye:	n/a
49	chr3:23247317-23247367	RPTEC	kidney:	n/a
50	chr3:23247317-23247367	HepG2	liver:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:23247004..23248744-chr3:23272999..23274643,2	K562	blood:
2	chr3:23243580..23246628-chr3:23247045..23250539,6	MCF-7	breast:
3	chr3:23245657..23247808-chr3:23255813..23257344,2	K562	blood:
4	chr3:23245705..23247404-chr3:23258369..23260756,2	K562	blood:
5	chr3:23244971..23246744-chr3:23246760..23249188,3	MCF-7	breast:
6	chr3:23245201..23247930-chr3:23252122..23255042,2	K562	blood:

No data

Variant related genes	Relation type
UBE2E2-AS1	TF binding region
UBE2E2-AS1	CpG island
ENSG00000182247	Chromatin interaction
ENSG00000233153	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17013009	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17013099	1.00[AMR][1000 genomes]
rs28548892	1.00[AMR][1000 genomes]
rs28641973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58879825	1.00[AMR][1000 genomes]
rs61636332	1.00[AMR][1000 genomes]
rs6768277	1.00[AMR][1000 genomes]
rs6795043	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73138415	1.00[AMR][1000 genomes]
rs73149654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73149686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73149689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7634565	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7646028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7652287	1.00[AMR][1000 genomes]
rs9310716	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9681506	1.00[AMR][1000 genomes]
rs9809364	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810378	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9811442	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9819788	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9821681	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9829577	1.00[AMR][1000 genomes]
rs9842159	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9861614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9878638	1.00[AMR][1000 genomes]
rs9879217	1.00[AMR][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	nsv999882	chr3:23121533-23257718	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23243800-23247400	Active TSS	GM12878-XiMat	blood
2	chr3:23245600-23251400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:23245600-23253400	Weak transcription	Lung	lung
4	chr3:23245800-23247800	Weak transcription	Small Intestine	intestine
5	chr3:23245800-23253200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:23245800-23262800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:23246000-23253000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:23246000-23260800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:23246200-23247400	Enhancers	Brain Cingulate Gyrus	brain
10	chr3:23246200-23247600	Weak transcription	Fetal Thymus	thymus
11	chr3:23246200-23247800	Weak transcription	Right Ventricle	heart
12	chr3:23246200-23248600	Weak transcription	Fetal Heart	heart
13	chr3:23246200-23251200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:23246200-23251200	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:23246200-23251200	Weak transcription	Psoas Muscle	Psoas
16	chr3:23246200-23252200	Weak transcription	Fetal Stomach	stomach
17	chr3:23246200-23257200	Weak transcription	Ovary	ovary
18	chr3:23246200-23257400	Weak transcription	Left Ventricle	heart
19	chr3:23246200-23258800	Weak transcription	HSMM	muscle
20	chr3:23246200-23259000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:23246200-23259000	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:23246200-23259200	Weak transcription	NH-A	brain
23	chr3:23246200-23260600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:23246200-23264200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:23246400-23248000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:23246400-23250000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:23246400-23250800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:23246400-23251000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:23246400-23251400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:23246400-23253200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:23246400-23259400	Weak transcription	Osteobl	bone
32	chr3:23246400-23261200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:23246400-23273400	Weak transcription	Aorta	Aorta
34	chr3:23246600-23247400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:23246600-23247400	Weak transcription	Brain Substantia Nigra	brain
36	chr3:23246600-23247400	Weak transcription	A549	lung
37	chr3:23246600-23247800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:23246600-23247800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:23246600-23247800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:23246600-23248000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr3:23246600-23248000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:23246600-23248000	Weak transcription	Thymus	Thymus
43	chr3:23246600-23248000	Weak transcription	HSMMtube	muscle
44	chr3:23246600-23248400	Enhancers	Primary B cells from cord blood	blood
45	chr3:23246600-23248800	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr3:23246600-23249200	Enhancers	Brain Hippocampus Middle	brain
47	chr3:23246600-23251200	Weak transcription	Adipose Nuclei	Adipose
48	chr3:23246600-23251200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:23246600-23251200	Weak transcription	HMEC	breast
50	chr3:23246600-23251400	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links