Variant report

Variant	rs2286378
Chromosome Location	chr12:1909979-1909980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:170)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:170 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:1909880-1910030	AG10803	skin:	n/a	n/a
2	CTCF	chr12:1909860-1910010	WERI-Rb-1	eye:	n/a	n/a
3	CTCF	chr12:1909880-1910030	AG04449	skin:	n/a	n/a
4	RAD21	chr12:1909809-1910162	HepG2	liver:	n/a	n/a
5	CTCF	chr12:1909874-1910064	Kidney_OC	kidney:	n/a	n/a
6	SMC3	chr12:1909919-1910126	K562	blood:	n/a	n/a
7	CTCF	chr12:1909804-1910068	GM19239	blood:	n/a	n/a
8	CTCF	chr12:1909860-1910010	AoAF	blood vessel:	n/a	n/a
9	CTCF	chr12:1909860-1910010	HPF	lung:	n/a	n/a
10	CTCF	chr12:1909880-1910030	HVMF	connective:	n/a	n/a
11	CTCF	chr12:1909880-1910030	HBMEC	blood vessel:	n/a	n/a
12	CTCF	chr12:1909860-1910010	HRPEpiC	eye:	n/a	n/a
13	CTCF	chr12:1909900-1910050	Caco-2	colon:	n/a	n/a
14	SMC3	chr12:1909812-1910120	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr12:1909778-1910052	T-47D	breast:	n/a	n/a
16	CTCF	chr12:1909757-1910178	IMR90	lung:	n/a	n/a
17	CTCF	chr12:1909865-1910083	Pancreas_OC	pancreas:	n/a	n/a
18	CTCF	chr12:1909900-1910050	HRE	kidney:	n/a	n/a
19	CTCF	chr12:1909860-1910010	NHLF	lung:	n/a	n/a
20	CEBPB	chr12:1909824-1910094	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr12:1909880-1910030	GM12870	blood:	n/a	n/a
22	CTCF	chr12:1909853-1910085	HepG2	liver:	n/a	n/a
23	MAX	chr12:1909781-1910612	NB4	blood:	n/a	chr12:1910335-1910345 chr12:1910251-1910261
24	CTCF	chr12:1909920-1910070	K562	blood:	n/a	n/a
25	CTCF	chr12:1909843-1910069	GM19240	blood:	n/a	n/a
26	ZNF143	chr12:1909814-1910193	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAZ	chr12:1909928-1910109	GM12878	blood:	n/a	n/a
28	CTCF	chr12:1909880-1910030	GM12865	blood:	n/a	n/a
29	RAD21	chr12:1909631-1910226	H1-hESC	embryonic stem cell:	n/a	chr12:1909733-1909746
30	CTCF	chr12:1909900-1910050	AG09319	gingival:	n/a	n/a
31	CTCF	chr12:1909880-1910030	GM12867	blood:	n/a	n/a
32	CTCF	chr12:1909900-1910050	AG04449	skin:	n/a	n/a
33	CTCF	chr12:1909880-1910030	HCM	heart:	n/a	n/a
34	CTCF	chr12:1909860-1910010	GM12871	blood:	n/a	n/a
35	CTCF	chr12:1909900-1910050	HA-sp	spinal cord:	n/a	n/a
36	CTCF	chr12:1909940-1910090	HPAF	blood vessel:	n/a	n/a
37	CTCF	chr12:1909826-1910138	K562	blood:	n/a	n/a
38	CTCF	chr12:1909860-1910010	GM12801	blood:	n/a	n/a
39	CTCF	chr12:1909839-1910072	GM12878	blood:	n/a	n/a
40	CTCF	chr12:1909880-1910030	GM12878	blood:	n/a	n/a
41	CTCF	chr12:1909880-1910030	GM12864	blood:	n/a	n/a
42	CTCF	chr12:1909852-1910085	GM20000	blood:	n/a	n/a
43	CTCF	chr12:1909920-1910070	GM12868	blood:	n/a	n/a
44	CTCF	chr12:1909860-1910010	HEK293	kidney:	n/a	n/a
45	CTCF	chr12:1909840-1909990	HRPEpiC	eye:	n/a	n/a
46	CTCF	chr12:1909940-1910090	GM12872	blood:	n/a	n/a
47	CTCF	chr12:1909920-1910070	A549	lung:	n/a	n/a
48	CTCF	chr12:1909824-1910174	H1-hESC	embryonic stem cell:	n/a	n/a
49	CEBPB	chr12:1909940-1910146	HepG2	liver:	n/a	n/a
50	CTCF	chr12:1909880-1910030	HCPEpiC	choroid plexus:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:1909928..1910790-chr12:2048924..2049519,2	K562	blood:

No data

Variant related genes	Relation type
CACNA2D4	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12580035	0.82[EUR][1000 genomes]
rs6489330	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv430442	chr12:1889823-1982151	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv556996	chr12:1891372-1934920	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1824001	chr12:1896738-1951940	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv898592	chr12:1901485-1937801	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv898593	chr12:1901485-1962759	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv468965	chr12:1907853-1931396	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv556997	chr12:1907853-1931396	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv468966	chr12:1907853-1933553	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv556998	chr12:1907853-1933553	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv470259	chr12:1907853-1945042	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1905600-1928600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:1905800-1913400	Weak transcription	HepG2	liver
3	chr12:1906000-1910000	Weak transcription	HSMM	muscle
4	chr12:1906400-1910400	Weak transcription	NH-A	brain
5	chr12:1906400-1913800	Weak transcription	Brain Angular Gyrus	brain
6	chr12:1906400-1913800	Weak transcription	Fetal Brain Male	brain
7	chr12:1906600-1910000	Weak transcription	Fetal Brain Female	brain
8	chr12:1906600-1910400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:1906600-1913600	Weak transcription	Brain Anterior Caudate	brain
10	chr12:1906600-1913800	Weak transcription	Primary T cells from cord blood	blood
11	chr12:1906800-1910000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:1906800-1912800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:1906800-1913800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:1906800-1913800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:1906800-1913800	Weak transcription	Brain Substantia Nigra	brain
16	chr12:1906800-1914000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:1906800-1914000	Weak transcription	Right Atrium	heart
18	chr12:1906800-1915400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:1907000-1913800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:1907200-1910200	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:1907200-1913000	Weak transcription	Right Ventricle	heart
22	chr12:1907200-1913400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:1907200-1913800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr12:1907200-1913800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:1907600-1913600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:1907800-1912800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:1907800-1913800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr12:1908000-1910400	Enhancers	Fetal Heart	heart
29	chr12:1908200-1911600	Weak transcription	Spleen	Spleen
30	chr12:1909200-1910600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:1909200-1910800	Enhancers	Primary B cells from peripheral blood	blood
32	chr12:1909200-1911600	Enhancers	NHDF-Ad	bronchial
33	chr12:1909400-1910000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:1909400-1910000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr12:1909400-1910400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:1909600-1910800	Enhancers	Primary B cells from cord blood	blood
37	chr12:1909600-1911000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:1909600-1911800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr12:1909800-1910000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:1909800-1910600	Enhancers	Osteobl	bone
41	chr12:1909800-1910800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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