Variant report

Variant	rs17279559
Chromosome Location	chr1:179836158-179836159
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	NR2F2	chr1:179835822-179836265	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:179835751-179836602	K562	blood:	n/a	n/a
3	GATA3	chr1:179835653-179836297	MCF-7	breast:	n/a	chr1:179835966-179835975
4	FOXA1	chr1:179835790-179836231	T-47D	breast:	n/a	chr1:179835853-179835865
5	GATA3	chr1:179835758-179836251	MCF-7	breast:	n/a	chr1:179835966-179835975
6	GATA3	chr1:179835810-179836298	SK-N-SH	brain:	n/a	chr1:179835966-179835975
7	GATA3	chr1:179835739-179836223	SK-N-SH	brain:	n/a	chr1:179835966-179835975
8	TEAD4	chr1:179835788-179836229	MCF-7	breast:	n/a	n/a
9	POLR2A	chr1:179835782-179837959	K562	blood:	n/a	n/a
10	CTCF	chr1:179836140-179836290	AG10803	skin:	n/a	n/a
11	EP300	chr1:179835765-179836179	T-47D	breast:	n/a	n/a
12	SIN3AK20	chr1:179835776-179836300	MCF-7	breast:	n/a	n/a
13	POLR2A	chr1:179835710-179836190	K562	blood:	n/a	n/a
14	CEBPB	chr1:179835746-179836228	MCF-7	breast:	n/a	n/a
15	GATA3	chr1:179835704-179836237	T-47D	breast:	n/a	chr1:179835966-179835975
16	POLR2A	chr1:179835887-179836686	HepG2	liver:	n/a	n/a
17	SIN3AK20	chr1:179835636-179836395	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179835375..179837616-chr1:179850235..179852594,3	MCF-7	breast:
2	chr1:179833882..179836832-chr1:180042170..180044941,2	K562	blood:
3	chr1:179832603..179840385-chr1:179843229..179848672,10	MCF-7	breast:
4	chr1:179834118..179836947-chr1:179843310..179847312,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258664	TF binding region
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000169905	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17279663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279684	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279712	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370777	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370826	0.86[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370847	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652455	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425595	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv519273	chr1:179831248-179847877	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17279559	CLEC4G	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179802400-179836200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:179808600-179837000	Strong transcription	Liver	Liver
3	chr1:179808600-179839800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:179812600-179842600	Weak transcription	Stomach Mucosa	stomach
5	chr1:179813200-179839200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:179814400-179839200	Strong transcription	HSMM	muscle
7	chr1:179815000-179839400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:179820400-179841400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:179820400-179841800	Weak transcription	Small Intestine	intestine
10	chr1:179820400-179844200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:179820400-179845400	Weak transcription	Right Ventricle	heart
12	chr1:179823000-179839200	Strong transcription	Osteobl	bone
13	chr1:179823800-179839200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr1:179823800-179843200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:179824200-179839800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:179824400-179837800	Strong transcription	Primary B cells from cord blood	blood
17	chr1:179824600-179838400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:179825000-179838200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr1:179825600-179839000	Strong transcription	Fetal Intestine Large	intestine
20	chr1:179825800-179839200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:179826200-179843400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:179828000-179845600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:179829200-179836600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:179829200-179838400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:179829400-179839000	Strong transcription	Dnd41	blood
26	chr1:179829600-179837000	Strong transcription	Adipose Nuclei	Adipose
27	chr1:179829600-179839200	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr1:179829600-179839400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:179829800-179840400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:179829800-179844800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:179830000-179839000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:179830000-179839200	Strong transcription	Hela-S3	cervix
33	chr1:179830200-179837800	Strong transcription	GM12878-XiMat	blood
34	chr1:179830200-179845200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:179830600-179839200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr1:179830800-179837000	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:179830800-179838800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr1:179830800-179839200	Strong transcription	HUVEC	blood vessel
39	chr1:179830800-179840400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:179830800-179842200	Strong transcription	K562	blood
41	chr1:179831000-179836800	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:179831000-179839200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:179831200-179837000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:179831200-179837000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:179831200-179838000	Strong transcription	A549	lung
46	chr1:179831200-179839200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:179831200-179845000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:179831400-179838000	Strong transcription	HepG2	liver
49	chr1:179831600-179836600	Strong transcription	Esophagus	oesophagus
50	chr1:179831600-179836800	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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