Variant report

Variant	rs56942518
Chromosome Location	chr12:49109236-49109237
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49109224-49111248	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:49108836-49111405	IMR90	lung:	n/a	n/a
3	GTF3C2	chr12:49109091-49110126	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr12:49109200-49109350	Caco-2	colon:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49109119..49112520-chr12:49258264..49261147,4	MCF-7	breast:
2	chr12:49103301..49108658-chr12:49108679..49112078,7	K562	blood:
3	chr12:49108930..49110553-chr12:49207843..49209517,2	MCF-7	breast:
4	chr12:49096349..49098245-chr12:49108578..49110236,2	K562	blood:
5	chr12:49072667..49077768-chr12:49107571..49112359,8	MCF-7	breast:
6	chr12:49108937..49110842-chr12:49180917..49183089,2	MCF-7	breast:
7	chr12:49108385..49110371-chr12:49210566..49212165,2	MCF-7	breast:
8	chr12:49073439..49079132-chr12:49108039..49112179,15	K562	blood:
9	chr12:49072639..49079132-chr12:49108469..49112073,12	K562	blood:
10	chr12:49072707..49077771-chr12:49103757..49111723,15	MCF-7	breast:

No data

Variant related genes	Relation type
CCNT1	TF binding region
ENSG00000139620	Chromatin interaction
ENSG00000257660	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000174233	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000129315	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs3902956	1.00[AFR][1000 genomes]
rs55823822	0.84[AFR][1000 genomes]
rs56015238	1.00[AFR][1000 genomes]
rs56037864	0.85[AFR][1000 genomes]
rs56306303	1.00[AFR][1000 genomes]
rs58685133	1.00[AFR][1000 genomes]
rs59636982	0.81[AFR][1000 genomes]
rs61522435	1.00[AFR][1000 genomes]
rs74088109	1.00[AFR][1000 genomes]
rs74088111	1.00[AFR][1000 genomes]
rs74088113	1.00[AFR][1000 genomes]
rs74088132	1.00[AFR][1000 genomes]
rs74088154	1.00[AFR][1000 genomes]
rs74088160	1.00[AFR][1000 genomes]
rs74088162	1.00[AFR][1000 genomes]
rs74089307	0.85[AFR][1000 genomes]
rs74089309	1.00[AFR][1000 genomes]
rs74089329	1.00[AFR][1000 genomes]
rs74089330	1.00[AFR][1000 genomes]
rs74089332	1.00[AFR][1000 genomes]
rs74089333	1.00[AFR][1000 genomes]
rs74089334	1.00[AFR][1000 genomes]
rs74089339	1.00[AFR][1000 genomes]
rs74089356	1.00[AFR][1000 genomes]
rs74089365	1.00[AFR][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	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 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	chr12:49089800-49109400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:49097600-49109400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:49098200-49109600	Weak transcription	Aorta	Aorta
4	chr12:49099600-49109400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:49105400-49109400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:49106400-49109400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:49107200-49109800	Enhancers	Small Intestine	intestine
8	chr12:49107200-49110400	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr12:49107600-49109400	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr12:49107600-49109400	Genic enhancers	Fetal Thymus	thymus
11	chr12:49107600-49109600	Enhancers	Brain Angular Gyrus	brain
12	chr12:49107600-49109600	Enhancers	Stomach Mucosa	stomach
13	chr12:49107600-49109800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:49107800-49109600	Enhancers	Fetal Heart	heart
15	chr12:49108000-49109400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:49108000-49109400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:49108000-49109600	Enhancers	Thymus	Thymus
18	chr12:49108200-49109400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:49108200-49111600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:49108400-49109600	Enhancers	Primary B cells from cord blood	blood
21	chr12:49108400-49109600	Enhancers	Fetal Brain Male	brain
22	chr12:49108400-49110000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:49108400-49110400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr12:49108600-49109600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr12:49108600-49109600	Enhancers	Primary T cells fromperipheralblood	blood
26	chr12:49108600-49109800	Enhancers	Esophagus	oesophagus
27	chr12:49108600-49110000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr12:49108600-49110000	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr12:49108600-49111800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:49108800-49109400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:49108800-49109400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:49108800-49109400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:49108800-49109600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:49108800-49109600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr12:49108800-49109600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr12:49108800-49109600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:49108800-49109600	Enhancers	Brain Hippocampus Middle	brain
38	chr12:49108800-49109600	Enhancers	Brain Substantia Nigra	brain
39	chr12:49108800-49109600	Active TSS	Colonic Mucosa	Colon
40	chr12:49108800-49109600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
41	chr12:49108800-49109800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:49108800-49109800	Enhancers	Spleen	Spleen
43	chr12:49108800-49110000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr12:49108800-49110000	Flanking Active TSS	Osteobl	bone
45	chr12:49108800-49110400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr12:49108800-49110400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:49108800-49111600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:49108800-49111600	Active TSS	NH-A	brain
49	chr12:49108800-49111600	Active TSS	NHLF	lung
50	chr12:49108800-49111800	Active TSS	iPS-18 Cell Line	embryonic stem cell

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