Variant report

Variant	rs3741974
Chromosome Location	chr12:1914273-1914274
allele	A/G
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	HCFC1	chr12:1913194-1914586	Hela-S3	cervix:	n/a	n/a
2	ELF1	chr12:1913539-1914291	HCT-116	colon:	n/a	chr12:1913868-1913881
3	E2F6	chr12:1913545-1914319	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF12	chr12:1913541-1914299	A549	lung:	n/a	chr12:1914079-1914087
5	GABPA	chr12:1913381-1914313	MCF-7	breast:	n/a	n/a
6	ELF1	chr12:1913555-1914283	MCF-7	breast:	n/a	chr12:1913868-1913881
7	POLR2A	chr12:1914257-1914313	HepG2	liver:	n/a	n/a
8	GABPA	chr12:1913516-1914283	SK-N-SH	brain:	n/a	n/a
9	ELF1	chr12:1913400-1914342	HCT-116	colon:	n/a	chr12:1913868-1913881
10	MAX	chr12:1913464-1914283	A549	lung:	n/a	chr12:1913782-1913792
11	ELF1	chr12:1913520-1914284	MCF-7	breast:	n/a	chr12:1913868-1913881
12	POLR2A	chr12:1913718-1914593	Raji	blood:	n/a	n/a
13	ELF1	chr12:1913704-1914540	GM12878	blood:	n/a	chr12:1913868-1913881
14	SREBP1	chr12:1913349-1914329	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:1913647-1914281	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:1913786..1914380-chr7:76038925..76039444,2	HCT-116	colon:
2	chr12:1911026..1914378-chr12:2033211..2036733,3	MCF-7	breast:
3	chr12:1912567..1917043-chr12:1917472..1921043,5	K562	blood:
4	chr12:1912567..1914410-chr12:1917472..1919007,2	K562	blood:
5	chr12:1908657..1911491-chr12:1913622..1915388,2	MCF-7	breast:
6	chr12:1905522..1910417-chr12:1912711..1915784,4	K562	blood:

Variant related genes	Relation type
CACNA2D4	TF binding region
ENSG00000146700	Chromatin interaction
ENSG00000151062	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12580035	0.90[CEU][hapmap]
rs6489330	1.00[CEU][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
14	nsv518013	chr12:1914273-1952990	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3741974	AKAP3	cis	cerebellum	SCAN
rs3741974	RAD51AP1	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1905600-1928600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:1906800-1915400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:1910000-1916400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:1910000-1916400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:1910800-1915000	Weak transcription	HSMMtube	muscle
6	chr12:1910800-1920000	Weak transcription	Primary B cells from cord blood	blood
7	chr12:1911200-1915400	Weak transcription	HSMM	muscle
8	chr12:1911600-1919200	Weak transcription	Osteobl	bone
9	chr12:1912800-1914600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr12:1912800-1917000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr12:1913200-1916200	Enhancers	Left Ventricle	heart
12	chr12:1913400-1914400	Enhancers	HepG2	liver
13	chr12:1913400-1917000	Enhancers	Duodenum Mucosa	Duodenum
14	chr12:1913600-1914400	Enhancers	Primary B cells from peripheral blood	blood
15	chr12:1913600-1914600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:1913800-1914400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:1913800-1914400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:1913800-1914400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:1913800-1914400	Enhancers	Fetal Brain Male	brain
20	chr12:1913800-1914400	Enhancers	Thymus	Thymus
21	chr12:1913800-1914400	Enhancers	GM12878-XiMat	blood
22	chr12:1913800-1914600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr12:1913800-1914800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr12:1913800-1916200	Enhancers	Fetal Muscle Trunk	muscle
25	chr12:1913800-1916400	Enhancers	Right Ventricle	heart
26	chr12:1913800-1916800	Enhancers	Fetal Muscle Leg	muscle
27	chr12:1913800-1917000	Enhancers	Fetal Intestine Large	intestine
28	chr12:1913800-1917600	Enhancers	Placenta	Placenta
29	chr12:1913800-1918800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr12:1913800-1920000	Enhancers	Fetal Thymus	thymus
31	chr12:1913800-1920400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:1914000-1914400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:1914000-1914400	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr12:1914000-1914400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:1914000-1914400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:1914000-1914400	Enhancers	Brain Hippocampus Middle	brain
37	chr12:1914000-1914600	Enhancers	Spleen	Spleen
38	chr12:1914000-1915000	Weak transcription	Stomach Mucosa	stomach
39	chr12:1914000-1915200	Enhancers	Right Atrium	heart
40	chr12:1914000-1916000	Enhancers	Adipose Nuclei	Adipose
41	chr12:1914000-1916000	Enhancers	Fetal Heart	heart
42	chr12:1914000-1917600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:1914000-1917600	Enhancers	Fetal Intestine Small	intestine
44	chr12:1914000-1920400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:1914200-1914400	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr12:1914200-1914400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr12:1914200-1914400	Enhancers	Brain Germinal Matrix	brain
48	chr12:1914200-1914400	Enhancers	Lung	lung
49	chr12:1914200-1915200	Weak transcription	NHDF-Ad	bronchial
50	chr12:1914200-1915600	Enhancers	Primary T cells fromperipheralblood	blood

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