Variant report

Variant	rs56265474
Chromosome Location	chr3:179095519-179095520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:179039914..179042763-chr3:179093091..179095772,2	K562	blood:
2	chr3:179064036..179066724-chr3:179094064..179095698,2	MCF-7	breast:
3	chr3:179095137..179097364-chr6:16950756..16952269,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171109	Chromatin interaction
ENSG00000121864	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11916825	0.89[AMR][1000 genomes]
rs11919840	0.89[AMR][1000 genomes]
rs11925064	0.89[AMR][1000 genomes]
rs11925248	0.89[AMR][1000 genomes]
rs11927084	0.89[AMR][1000 genomes]
rs13317510	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13320472	0.81[AMR][1000 genomes]
rs16830445	1.00[AMR][1000 genomes]
rs16830460	1.00[AMR][1000 genomes]
rs28512433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28522651	0.89[AMR][1000 genomes]
rs55805052	0.89[AMR][1000 genomes]
rs56280435	0.89[AMR][1000 genomes]
rs57148977	0.89[AMR][1000 genomes]
rs57526364	0.89[AMR][1000 genomes]
rs57795346	0.89[AMR][1000 genomes]
rs58741861	1.00[AMR][1000 genomes]
rs59062224	0.89[AMR][1000 genomes]
rs59333548	1.00[AMR][1000 genomes]
rs59511701	0.89[AMR][1000 genomes]
rs59564372	0.89[AMR][1000 genomes]
rs60191176	0.89[AMR][1000 genomes]
rs60746059	0.89[AMR][1000 genomes]
rs61246771	1.00[AMR][1000 genomes]
rs61325843	0.89[AMR][1000 genomes]
rs6778235	1.00[AMR][1000 genomes]
rs6800044	1.00[AMR][1000 genomes]
rs6808033	1.00[AMR][1000 genomes]
rs6808866	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043406	0.89[AMR][1000 genomes]
rs73043407	0.89[AMR][1000 genomes]
rs73043413	0.89[AMR][1000 genomes]
rs73045191	1.00[AMR][1000 genomes]
rs73045195	1.00[AMR][1000 genomes]
rs73045198	1.00[AMR][1000 genomes]
rs73059758	0.89[AMR][1000 genomes]
rs73059766	0.89[AMR][1000 genomes]
rs7355835	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883508	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73886620	0.89[AMR][1000 genomes]
rs7611533	1.00[AMR][1000 genomes]
rs7625719	0.89[AMR][1000 genomes]
rs9814990	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9815687	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9829054	1.00[AMR][1000 genomes]
rs9834493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861354	1.00[AMR][1000 genomes]
rs9864857	1.00[AMR][1000 genomes]
rs9872939	1.00[AMR][1000 genomes]
rs9884070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9968068	0.89[AMR][1000 genomes]
rs9968069	0.89[AMR][1000 genomes]
rs9968075	0.89[AMR][1000 genomes]
rs9968076	0.89[AMR][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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1002962	chr3:178943753-179224548	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv536815	chr3:178943753-179224548	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv1003021	chr3:178944806-179246179	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv1006584	chr3:178944822-179241429	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv829806	chr3:178952363-179154373	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv471116	chr3:178968634-179252263	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv592650	chr3:178968634-179252263	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv1010513	chr3:178976107-179196274	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536816	chr3:178976107-179196274	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1003514	chr3:178990037-179177029	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179066400-179136600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:179066800-179104200	Weak transcription	Fetal Heart	heart
3	chr3:179066800-179113600	Weak transcription	Stomach Mucosa	stomach
4	chr3:179066800-179118800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:179067000-179097600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:179067000-179099800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:179067000-179099800	Strong transcription	HSMM	muscle
8	chr3:179067200-179131200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:179067800-179099600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:179068000-179099600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:179068600-179099800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:179070600-179120000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:179072000-179098000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:179076400-179110600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:179080200-179099800	Strong transcription	Fetal Thymus	thymus
16	chr3:179081400-179138000	Weak transcription	Colonic Mucosa	Colon
17	chr3:179081600-179095800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:179081600-179095800	Weak transcription	Small Intestine	intestine
19	chr3:179081600-179096000	Weak transcription	Brain Germinal Matrix	brain
20	chr3:179081600-179096800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:179081600-179096800	Weak transcription	Pancreas	Pancrea
22	chr3:179081600-179113400	Weak transcription	Gastric	stomach
23	chr3:179081600-179115200	Weak transcription	Spleen	Spleen
24	chr3:179081600-179120400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:179084000-179096000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
27	chr3:179084600-179104000	Weak transcription	A549	lung
28	chr3:179084800-179096800	Weak transcription	Brain Angular Gyrus	brain
29	chr3:179085400-179096200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:179085400-179096200	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:179085400-179104400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:179085400-179111400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:179087200-179096200	Weak transcription	Brain Anterior Caudate	brain
34	chr3:179087200-179096800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:179087200-179122800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:179087600-179095800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:179087600-179096400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:179087600-179120000	Weak transcription	Right Ventricle	heart
39	chr3:179088400-179141800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:179088600-179095600	Weak transcription	Lung	lung
41	chr3:179088600-179115400	Weak transcription	Aorta	Aorta
42	chr3:179089000-179096200	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:179089400-179096800	Weak transcription	Ovary	ovary
44	chr3:179089400-179104200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:179090600-179099600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr3:179092200-179099400	Strong transcription	Placenta	Placenta
47	chr3:179092200-179099600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:179092200-179099600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:179092400-179098000	Strong transcription	GM12878-XiMat	blood
50	chr3:179092400-179099600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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