Variant report

Variant	rs28522651
Chromosome Location	chr3:179053768-179053769
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:179053708-179053981	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:179050819-179054775	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:179052233..179055645-chr3:179056953..179060224,5	K562	blood:
2	chr3:179052189..179054358-chr3:196065129..196066757,2	K562	blood:
3	chr3:179045767..179049611-chr3:179051935..179054562,3	MCF-7	breast:
4	chr3:179051441..179053833-chr3:179297266..179300130,2	K562	blood:
5	chr3:179040837..179042688-chr3:179052036..179053996,2	K562	blood:
6	chr3:179050239..179054117-chr3:179056953..179060377,5	K562	blood:
7	chr3:179039578..179042540-chr3:179052637..179054150,2	MCF-7	breast:
8	chr3:179050479..179052351-chr3:179053521..179055671,2	K562	blood:
9	chr3:179051794..179054722-chr3:179061170..179063608,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000273190	TF binding region
ENSG00000260743	TF binding region
ENSG00000145107	Chromatin interaction
ENSG00000121864	Chromatin interaction
ENSG00000273331	Chromatin interaction
ENSG00000136518	Chromatin interaction
ENSG00000260743	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11916825	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11919840	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11925064	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11925248	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11927084	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13317510	0.89[AMR][1000 genomes]
rs16830445	0.89[AMR][1000 genomes]
rs16830460	0.89[AMR][1000 genomes]
rs28512433	0.89[AMR][1000 genomes]
rs55805052	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56210820	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56265474	0.89[AMR][1000 genomes]
rs56280435	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57148977	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57526364	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57795346	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58741861	0.89[AMR][1000 genomes]
rs59062224	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59333548	0.89[AMR][1000 genomes]
rs59511701	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59564372	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59833817	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60191176	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60746059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61246771	0.89[AMR][1000 genomes]
rs61325843	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6778235	0.89[AMR][1000 genomes]
rs6800044	0.89[AMR][1000 genomes]
rs6808033	0.89[AMR][1000 genomes]
rs6808866	1.00[AMR][1000 genomes]
rs73043406	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043409	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73043413	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043415	0.96[AFR][1000 genomes]
rs73045191	0.89[AMR][1000 genomes]
rs73045195	0.89[AMR][1000 genomes]
rs73045198	0.89[AMR][1000 genomes]
rs73059758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73059766	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7355835	0.89[AMR][1000 genomes]
rs73883508	0.89[AMR][1000 genomes]
rs73883509	0.89[AMR][1000 genomes]
rs73886620	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7611533	0.89[AMR][1000 genomes]
rs7625719	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814990	0.89[AMR][1000 genomes]
rs9829054	0.89[AMR][1000 genomes]
rs9834493	0.89[AMR][1000 genomes]
rs9861354	0.89[AMR][1000 genomes]
rs9864857	0.89[AMR][1000 genomes]
rs9872939	0.89[AMR][1000 genomes]
rs9884070	0.89[AMR][1000 genomes]
rs9968068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968076	1.00[AMR][1000 genomes];1.00[EUR][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	chr3:179042600-179054000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:179043000-179054800	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:179043000-179054800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:179043000-179055600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:179043200-179054600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:179043200-179056200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:179043200-179057000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:179043200-179057400	Strong transcription	Fetal Intestine Large	intestine
9	chr3:179043400-179054200	Strong transcription	Osteobl	bone
10	chr3:179043400-179054600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:179043400-179055200	Strong transcription	Fetal Thymus	thymus
12	chr3:179043400-179056600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:179043400-179057200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:179043400-179065200	Weak transcription	Stomach Mucosa	stomach
15	chr3:179043600-179054800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:179043800-179054600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:179043800-179057200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:179044400-179054800	Strong transcription	Dnd41	blood
19	chr3:179044600-179056400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:179044800-179054800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:179045000-179054600	Strong transcription	Hela-S3	cervix
22	chr3:179045000-179054800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:179045000-179054800	Strong transcription	HSMM	muscle
24	chr3:179045200-179053800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:179045200-179054800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:179045200-179054800	Strong transcription	Brain Anterior Caudate	brain
27	chr3:179045400-179054400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:179045400-179054600	Strong transcription	NH-A	brain
29	chr3:179045400-179057400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:179045600-179054600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:179045600-179054800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr3:179045600-179054800	Strong transcription	Liver	Liver
33	chr3:179045600-179054800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:179045800-179054400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr3:179045800-179054600	Strong transcription	HUVEC	blood vessel
36	chr3:179045800-179054800	Strong transcription	Adipose Nuclei	Adipose
37	chr3:179045800-179055000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:179045800-179055600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:179046000-179054600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:179046000-179054800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:179046000-179054800	Strong transcription	HMEC	breast
42	chr3:179046200-179054600	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr3:179046200-179055400	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr3:179046200-179055800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:179046200-179055800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:179046400-179054600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:179046400-179054600	Strong transcription	Brain Hippocampus Middle	brain
48	chr3:179046400-179054800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:179046400-179054800	Strong transcription	Fetal Brain Female	brain
50	chr3:179046400-179057200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links