Variant report

Variant	rs2477117
Chromosome Location	chr1:179992076-179992077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179922853..179925382-chr1:179991871..179994080,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260360	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10798729	0.80[JPT][hapmap]
rs10913916	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10913917	0.81[JPT][hapmap]
rs10913918	0.84[CEU][hapmap]
rs10913927	0.93[JPT][hapmap]
rs12075450	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs12091685	0.81[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap]
rs16855164	0.92[ASN][1000 genomes]
rs1981314	0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2319676	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2319677	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs2319773	0.83[ASN][1000 genomes]
rs2477106	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2477107	0.90[ASN][1000 genomes]
rs2477109	0.88[ASN][1000 genomes]
rs2477111	0.81[JPT][hapmap]
rs2477112	0.81[JPT][hapmap]
rs2477113	0.86[ASN][1000 genomes]
rs2477115	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2477118	0.81[JPT][hapmap]
rs2477119	0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2483622	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2501608	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2501611	0.81[JPT][hapmap]
rs2501613	0.81[JPT][hapmap]
rs2501614	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2501615	0.81[JPT][hapmap]
rs2501618	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2501619	0.85[ASN][1000 genomes]
rs2501621	0.87[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2762859	0.81[JPT][hapmap]
rs3123521	0.91[ASN][1000 genomes]
rs3767201	0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs3818999	0.81[JPT][hapmap]
rs3930305	0.93[JPT][hapmap]
rs4076449	0.93[JPT][hapmap]
rs4147170	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs4256775	0.93[JPT][hapmap]
rs4263962	0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4379644	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4622030	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs4651055	0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4652461	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652464	0.83[ASN][1000 genomes]
rs4652465	0.93[JPT][hapmap]
rs483307	0.81[JPT][hapmap]
rs510209	0.81[JPT][hapmap]
rs551607	0.81[ASW][hapmap]
rs552743	0.84[CEU][hapmap]
rs55953436	0.84[EUR][1000 genomes]
rs55971224	0.83[EUR][1000 genomes]
rs6425602	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425603	0.93[JPT][hapmap]
rs6425606	0.90[ASW][hapmap];0.89[CEU][hapmap];0.85[JPT][hapmap]
rs6425607	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs6657347	0.93[JPT][hapmap]
rs6659911	0.88[ASN][1000 genomes]
rs6660984	0.80[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6676989	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682558	0.88[CEU][hapmap]
rs6692394	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7521948	1.00[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9286932	0.93[JPT][hapmap]
rs9425849	0.93[JPT][hapmap]
rs9425852	0.91[ASN][1000 genomes]
rs9425853	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9425854	0.93[JPT][hapmap]
rs9425857	0.86[ASN][1000 genomes]
rs9425858	0.82[ASN][1000 genomes]
rs9425859	0.87[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs9425861	0.93[JPT][hapmap]
rs9887843	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
2	chr1:179964000-180014200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:179965800-180013200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr1:179971600-179997400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr1:179973000-180010800	Weak transcription	Psoas Muscle	Psoas
7	chr1:179976200-180063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:179979400-179999600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:179979600-180002000	Strong transcription	Fetal Intestine Large	intestine
10	chr1:179979800-179998000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:179979800-179998600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:179979800-179999000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:179979800-179999400	Strong transcription	Fetal Thymus	thymus
14	chr1:179979800-180008400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:179980200-180007800	Strong transcription	Primary B cells from cord blood	blood
16	chr1:179980400-179994000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:179980400-179998200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:179980400-180027400	Strong transcription	Dnd41	blood
19	chr1:179980600-179997400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:179980600-179999000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:179980600-179999200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:179980600-179999800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:179980600-180008000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:179981000-179995800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:179981000-179997000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:179981000-180027200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr1:179981000-180059000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:179981200-179996400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:179981200-179996800	Strong transcription	Adipose Nuclei	Adipose
30	chr1:179981400-179995200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:179981600-179992600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:179981600-179997400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:179981600-179997600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:179981600-179998000	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:179981600-180012000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:179982400-179993200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:179982400-179996400	Strong transcription	Placenta	Placenta
38	chr1:179982400-179998000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr1:179982400-179999000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:179982600-179993800	Strong transcription	GM12878-XiMat	blood
41	chr1:179982600-179994800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:179982800-179994600	Strong transcription	Osteobl	bone
43	chr1:179983000-179992600	Strong transcription	Fetal Muscle Leg	muscle
44	chr1:179983000-179995400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:179983000-179996000	Strong transcription	Liver	Liver
46	chr1:179983000-179996400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:179983000-179996600	Strong transcription	Hela-S3	cervix
48	chr1:179983000-179998800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:179983000-179999000	Strong transcription	Primary T cells from cord blood	blood
50	chr1:179983200-179992600	Strong transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links