Variant report

Variant	rs55916159
Chromosome Location	chr12:49204644-49204645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr12:49204610-49205228	HepG2	liver:	n/a	n/a
2	MAX	chr12:49204508-49205480	A549	lung:	n/a	n/a
3	EP300	chr12:49204641-49205004	HepG2	liver:	n/a	chr12:49204762-49204775
4	CEBPB	chr12:49204618-49204921	HepG2	liver:	n/a	chr12:49204748-49204765
5	FOXA2	chr12:49204561-49205385	HepG2	liver:	n/a	n/a
6	MAZ	chr12:49203806-49206443	IMR90	lung:	n/a	n/a
7	CEBPB	chr12:49204591-49205173	IMR90	lung:	n/a	chr12:49204748-49204765
8	SP1	chr12:49204581-49205166	HepG2	liver:	n/a	chr12:49205069-49205083 chr12:49205075-49205089 chr12:49205001-49205015
9	TCF12	chr12:49204474-49205417	A549	lung:	n/a	chr12:49205025-49205035 chr12:49204888-49204895 chr12:49205049-49205058
10	SP1	chr12:49204589-49205393	A549	lung:	n/a	chr12:49205069-49205083 chr12:49205075-49205089 chr12:49205001-49205015
11	SP1	chr12:49204564-49205396	A549	lung:	n/a	chr12:49205069-49205083 chr12:49205075-49205089 chr12:49205001-49205015
12	ATF3	chr12:49204632-49204895	HepG2	liver:	n/a	n/a
13	RCOR1	chr12:49204192-49206087	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49203980..49213270-chr12:49239370..49250118,15	MCF-7	breast:
2	chr12:49182132..49185770-chr12:49202933..49205906,3	MCF-7	breast:
3	chr12:49073658..49078597-chr12:49201352..49212442,12	MCF-7	breast:

Variant related genes	Relation type
CACNB3	TF binding region
ENSG00000257660	Chromatin interaction
ENSG00000174233	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000139620	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11168749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168751	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369114	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369130	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12814893	1.00[ASN][1000 genomes]
rs2453467	1.00[ASN][1000 genomes]
rs34014405	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36000595	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3730308	1.00[ASN][1000 genomes]
rs55638074	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][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	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55916159	CACNB3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49201200-49207600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:49201600-49207600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:49203600-49207600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr12:49203800-49205600	Enhancers	Fetal Kidney	kidney
5	chr12:49203800-49205800	Enhancers	Stomach Smooth Muscle	stomach
6	chr12:49204000-49204800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:49204000-49205400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:49204000-49205600	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr12:49204000-49205800	Enhancers	Fetal Intestine Large	intestine
10	chr12:49204000-49205800	Enhancers	Fetal Lung	lung
11	chr12:49204000-49206400	Enhancers	Fetal Intestine Small	intestine
12	chr12:49204000-49207200	Enhancers	Ovary	ovary
13	chr12:49204000-49207400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:49204200-49204800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:49204200-49204800	Enhancers	A549	lung
16	chr12:49204200-49205200	Flanking Active TSS	HepG2	liver
17	chr12:49204200-49205400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:49204200-49205400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:49204200-49205400	Enhancers	Stomach Mucosa	stomach
20	chr12:49204200-49205800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:49204200-49206000	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr12:49204200-49206200	Enhancers	Duodenum Mucosa	Duodenum
23	chr12:49204200-49206200	Enhancers	HSMMtube	muscle
24	chr12:49204200-49206400	Enhancers	Fetal Stomach	stomach
25	chr12:49204200-49206600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:49204200-49206800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:49204200-49207600	Enhancers	Fetal Muscle Trunk	muscle
28	chr12:49204200-49207600	Enhancers	Placenta	Placenta
29	chr12:49204400-49204800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
30	chr12:49204400-49204800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:49204400-49205000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
32	chr12:49204400-49205000	Flanking Active TSS	NHLF	lung
33	chr12:49204400-49205200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr12:49204400-49205600	Enhancers	Gastric	stomach
35	chr12:49204400-49205800	Enhancers	Colonic Mucosa	Colon
36	chr12:49204400-49206200	Enhancers	Fetal Muscle Leg	muscle
37	chr12:49204400-49206200	Enhancers	Lung	lung
38	chr12:49204400-49206200	Enhancers	NHDF-Ad	bronchial
39	chr12:49204400-49206600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:49204600-49204800	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr12:49204600-49204800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:49204600-49204800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:49204600-49204800	Enhancers	Esophagus	oesophagus
44	chr12:49204600-49204800	Enhancers	Right Atrium	heart
45	chr12:49204600-49205000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:49204600-49205000	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr12:49204600-49205600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:49204600-49205600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:49204600-49205600	Flanking Active TSS	NH-A	brain
50	chr12:49204600-49205800	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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