Variant report

Variant	rs12751064
Chromosome Location	chr1:78006124-78006125
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	STAT3	chr1:78005490-78006599	Hela-S3	cervix:	n/a	chr1:78006375-78006384
2	MXI1	chr1:78005731-78006460	Hela-S3	cervix:	n/a	n/a
3	STAT1	chr1:78004728-78006805	Hela-S3	cervix:	n/a	chr1:78006375-78006384
4	GTF3C2	chr1:78006056-78006938	Hela-S3	cervix:	n/a	n/a
5	EBF1	chr1:78006102-78006527	GM12878	blood:	n/a	chr1:78006303-78006314
6	NFIC	chr1:78006119-78006620	ECC-1	luminal epithelium:	n/a	n/a
7	CEBPB	chr1:78005674-78006766	A549	lung:	n/a	n/a
8	MYC	chr1:78006069-78006595	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:78004473-78006648	U87	brain:	n/a	n/a
10	SMARCC1	chr1:78004743-78006663	Hela-S3	cervix:	n/a	n/a
11	TCF12	chr1:78004364-78006643	A549	lung:	n/a	n/a
12	TFAP2C	chr1:78005012-78006925	Hela-S3	cervix:	n/a	n/a
13	JUND	chr1:78005452-78006624	Hela-S3	cervix:	n/a	chr1:78005610-78005619 chr1:78006376-78006383
14	GATA3	chr1:78004360-78006650	A549	lung:	n/a	n/a
15	MAFK	chr1:78005431-78006272	Hela-S3	cervix:	n/a	chr1:78005622-78005631 chr1:78005615-78005635 chr1:78005621-78005631 chr1:78005617-78005633
16	TBP	chr1:78005461-78006550	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:78004532-78006692	U87	brain:	n/a	n/a
18	CEBPB	chr1:78004592-78006983	Hela-S3	cervix:	n/a	n/a
19	EP300	chr1:78005436-78006603	Hela-S3	cervix:	n/a	chr1:78005869-78005882 chr1:78006398-78006412
20	TCF12	chr1:78004404-78006421	SK-N-SH	brain:	n/a	n/a
21	MAX	chr1:78005343-78006559	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr1:78006039-78006630	A549	lung:	n/a	n/a
23	RCOR1	chr1:78004955-78006618	Hela-S3	cervix:	n/a	n/a
24	JUN	chr1:78006090-78006534	Hela-S3	cervix:	n/a	chr1:78006376-78006383
25	CHD2	chr1:78006123-78006503	Hela-S3	cervix:	n/a	n/a
26	SP1	chr1:78006067-78006590	A549	lung:	n/a	n/a
27	TCF7L2	chr1:78005289-78006929	Hela-S3	cervix:	n/a	chr1:78006375-78006384
28	FOSL2	chr1:78006104-78006624	A549	lung:	n/a	chr1:78006376-78006383
29	EBF1	chr1:78006095-78006494	GM12878	blood:	n/a	chr1:78006303-78006314
30	EP300	chr1:78005965-78006503	GM12878	blood:	n/a	chr1:78006398-78006412
31	MAX	chr1:78005440-78006542	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr1:78004477-78006805	U87	brain:	n/a	n/a
33	SMC3	chr1:78006059-78006523	Hela-S3	cervix:	n/a	n/a
34	MAX	chr1:78006103-78006411	A549	lung:	n/a	n/a
35	MAZ	chr1:78005315-78006414	Hela-S3	cervix:	n/a	n/a
36	FOSL1	chr1:78006107-78006635	HCT-116	colon:	n/a	chr1:78006376-78006383
37	RFX5	chr1:78005981-78006507	Hela-S3	cervix:	n/a	n/a
38	TFAP2A	chr1:78005423-78006572	Hela-S3	cervix:	n/a	chr1:78005707-78005719
39	POLR2A	chr1:78004471-78006766	U87	brain:	n/a	n/a
40	GTF2F1	chr1:78005487-78006496	Hela-S3	cervix:	n/a	n/a
41	EBF1	chr1:78005623-78006540	GM12878	blood:	n/a	chr1:78006303-78006314
42	EP300	chr1:78006050-78006707	ECC-1	luminal epithelium:	n/a	chr1:78006398-78006412

Variant related genes	Relation type
AK5	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12402928	1.00[ASN][1000 genomes]
rs12409142	1.00[ASN][1000 genomes]
rs12728967	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12733666	1.00[CHD][hapmap]
rs12741347	1.00[ASN][1000 genomes]
rs1377737	1.00[JPT][hapmap]
rs17098287	1.00[JPT][hapmap]
rs17100463	1.00[JPT][hapmap]
rs17100476	1.00[JPT][hapmap]
rs17381664	1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1909202	1.00[CHD][hapmap]
rs1909203	1.00[CHD][hapmap]
rs1963170	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2647497	1.00[CHD][hapmap]
rs4949660	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4949662	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4949803	1.00[CHD][hapmap]
rs6678622	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6684022	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv871143	chr1:77955577-78031994	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1533	chr1:77990504-78036279	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12751064	IFI44	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77983000-78009200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:77998000-78014000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:77999600-78009600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:78000000-78011600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:78000000-78030600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:78000000-78031200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:78000800-78006800	Strong transcription	Primary T cells from cord blood	blood
8	chr1:78001400-78006600	Enhancers	NHEK	skin
9	chr1:78001600-78006200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:78001600-78006600	Enhancers	HMEC	breast
11	chr1:78001800-78006600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:78004200-78007800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:78004400-78006200	Enhancers	Stomach Mucosa	stomach
14	chr1:78004400-78006200	Flanking Active TSS	A549	lung
15	chr1:78004400-78006400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:78004400-78007600	Enhancers	GM12878-XiMat	blood
17	chr1:78004600-78006200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:78004600-78006200	Enhancers	Brain Cingulate Gyrus	brain
19	chr1:78004600-78006200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr1:78004600-78006400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:78004600-78006600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:78004600-78006600	Flanking Active TSS	Osteobl	bone
23	chr1:78004600-78008200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:78004800-78006200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:78004800-78006200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:78004800-78006200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:78004800-78006400	Flanking Active TSS	Hela-S3	cervix
28	chr1:78004800-78006600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:78004800-78007400	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr1:78004800-78010800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:78005000-78006200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:78005000-78006200	Enhancers	Gastric	stomach
33	chr1:78005000-78006200	Enhancers	HSMMtube	muscle
34	chr1:78005000-78006400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:78005000-78006600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr1:78005000-78007400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:78005200-78006200	Enhancers	Lung	lung
38	chr1:78005200-78007400	Enhancers	Placenta	Placenta
39	chr1:78005200-78008000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:78005400-78006400	Enhancers	Primary hematopoietic stem cells	blood
41	chr1:78005400-78006600	Enhancers	NHLF	lung
42	chr1:78005400-78006800	Enhancers	NHDF-Ad	bronchial
43	chr1:78005400-78007000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr1:78005400-78007000	Weak transcription	Fetal Kidney	kidney
45	chr1:78005400-78007600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:78005600-78007400	Enhancers	Primary B cells from peripheral blood	blood
47	chr1:78005600-78010200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:78005600-78010400	Weak transcription	Fetal Heart	heart
49	chr1:78005600-78014000	Weak transcription	Right Ventricle	heart
50	chr1:78005600-78034800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links