Variant report

Variant	rs57440640
Chromosome Location	chr3:52565418-52565419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52565380-52565815	K562	blood:	n/a	n/a
2	POLR2A	chr3:52564728-52566280	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:52563501-52565690	U87	brain:	n/a	n/a
4	POLR2A	chr3:52564920-52565514	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:52565324-52565460	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:52563182-52567206	K562	blood:	n/a	n/a
7	POLR2A	chr3:52564880-52565486	GM12892	blood:	n/a	n/a
8	POLR2A	chr3:52560598-52572342	HepG2	liver:	n/a	n/a
9	ZNF263	chr3:52565405-52565600	HEK293-T-REx	kidney:	n/a	n/a
10	POLR2A	chr3:52563396-52565690	U87	brain:	n/a	n/a
11	POLR2A	chr3:52564917-52567026	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr3:52564832-52568664	K562	blood:	n/a	n/a
13	POLR2A	chr3:52565286-52565561	U87	brain:	n/a	n/a
14	POLR2A	chr3:52565227-52568334	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr3:52564773-52569282	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52489605..52491332-chr3:52564945..52566721,2	K562	blood:
2	chr3:52508946..52511340-chr3:52565152..52566782,2	MCF-7	breast:
3	chr3:52513829..52516090-chr3:52563915..52565701,2	MCF-7	breast:
4	chr3:52555579..52557218-chr3:52564676..52566664,2	MCF-7	breast:
5	chr3:52559482..52561203-chr3:52562436..52565441,3	MCF-7	breast:

No data

Variant related genes	Relation type
SMIM4	TF binding region
NT5DC2	TF binding region
ENSG00000010327	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000168268	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17052269	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052322	1.00[AMR][1000 genomes]
rs17052355	1.00[AMR][1000 genomes]
rs1971811	1.00[AMR][1000 genomes]
rs41415947	1.00[AMR][1000 genomes]
rs56815357	1.00[AMR][1000 genomes]
rs57401769	1.00[AMR][1000 genomes]
rs58242587	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59078569	0.91[AFR][1000 genomes]
rs59410274	0.91[AFR][1000 genomes]
rs59789322	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60351358	1.00[AMR][1000 genomes]
rs60404983	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60832323	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61418167	0.91[AFR][1000 genomes]
rs61484330	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv876796	chr3:52549676-52572056	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:52550600-52566600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:52552800-52566000	Weak transcription	Stomach Mucosa	stomach
4	chr3:52552800-52566200	Weak transcription	Brain Angular Gyrus	brain
5	chr3:52554200-52566000	Weak transcription	HSMM	muscle
6	chr3:52554800-52567200	Weak transcription	Aorta	Aorta
7	chr3:52556000-52566000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:52556800-52566400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:52557000-52565800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:52557400-52565800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:52558200-52566200	Genic enhancers	Fetal Lung	lung
12	chr3:52558400-52566200	Weak transcription	Fetal Kidney	kidney
13	chr3:52558400-52566200	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr3:52558400-52567000	Weak transcription	Small Intestine	intestine
15	chr3:52558600-52566200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:52558600-52566600	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:52558800-52566400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:52558800-52566600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:52559000-52566800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:52559200-52565800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:52559800-52566400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:52560000-52566000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:52560200-52566600	Weak transcription	Liver	Liver
24	chr3:52560600-52566800	Weak transcription	HSMMtube	muscle
25	chr3:52561400-52565800	Weak transcription	Hela-S3	cervix
26	chr3:52562000-52566000	Weak transcription	HMEC	breast
27	chr3:52562200-52566000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr3:52562200-52566000	Weak transcription	Pancreas	Pancrea
29	chr3:52562400-52566000	Weak transcription	Brain Substantia Nigra	brain
30	chr3:52562400-52566400	Weak transcription	Thymus	Thymus
31	chr3:52562600-52565800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:52562600-52566600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:52562800-52566600	Enhancers	Fetal Heart	heart
34	chr3:52562800-52566600	Weak transcription	Gastric	stomach
35	chr3:52562800-52566600	Enhancers	Right Atrium	heart
36	chr3:52563000-52566000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:52563000-52566800	Enhancers	Lung	lung
38	chr3:52563200-52565800	Weak transcription	Fetal Thymus	thymus
39	chr3:52563200-52566000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:52563200-52566400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:52563200-52566600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr3:52563400-52565800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52563400-52565800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:52563400-52565800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:52563400-52566000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:52563400-52566000	Weak transcription	A549	lung
47	chr3:52563400-52566200	Enhancers	Adipose Nuclei	Adipose
48	chr3:52563400-52566200	Weak transcription	Fetal Intestine Large	intestine
49	chr3:52563400-52566200	Genic enhancers	Fetal Stomach	stomach
50	chr3:52563400-52566600	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links