Variant report

Variant	rs59062224
Chromosome Location	chr3:179050859-179050860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:179039713..179044210-chr3:179048103..179052348,6	MCF-7	breast:
2	chr3:179050614..179052901-chr3:179085882..179088526,2	K562	blood:
3	chr3:179050479..179052351-chr3:179053521..179055671,2	K562	blood:
4	chr3:179050239..179054117-chr3:179056953..179060377,5	K562	blood:
5	chr3:179040634..179042276-chr3:179050547..179052585,2	MCF-7	breast:
6	chr3:179039098..179043202-chr3:179047493..179051938,6	K562	blood:
7	chr3:179043342..179045158-chr3:179050500..179053191,2	K562	blood:

Variant related genes	Relation type
ENSG00000260743	Chromatin interaction
ENSG00000121864	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	1.00[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]
rs28522651	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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]
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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179042400-179051800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:179042600-179054000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:179043000-179054800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:179043000-179054800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:179043000-179055600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:179043200-179051400	Weak transcription	Fetal Heart	heart
7	chr3:179043200-179053200	Strong transcription	Placenta	Placenta
8	chr3:179043200-179054600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:179043200-179056200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:179043200-179057000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:179043200-179057400	Strong transcription	Fetal Intestine Large	intestine
12	chr3:179043400-179054200	Strong transcription	Osteobl	bone
13	chr3:179043400-179054600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:179043400-179055200	Strong transcription	Fetal Thymus	thymus
15	chr3:179043400-179056600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:179043400-179057200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:179043400-179065200	Weak transcription	Stomach Mucosa	stomach
18	chr3:179043600-179054800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:179043800-179054600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:179043800-179057200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:179044400-179054800	Strong transcription	Dnd41	blood
22	chr3:179044600-179056400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:179044800-179054800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:179045000-179054600	Strong transcription	Hela-S3	cervix
25	chr3:179045000-179054800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:179045000-179054800	Strong transcription	HSMM	muscle
27	chr3:179045200-179052200	Strong transcription	Primary hematopoietic stem cells	blood
28	chr3:179045200-179053800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:179045200-179054800	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr3:179045200-179054800	Strong transcription	Brain Anterior Caudate	brain
31	chr3:179045400-179051800	Strong transcription	Primary T cells from cord blood	blood
32	chr3:179045400-179052400	Strong transcription	A549	lung
33	chr3:179045400-179054400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:179045400-179054600	Strong transcription	NH-A	brain
35	chr3:179045400-179057400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:179045600-179053000	Strong transcription	NHDF-Ad	bronchial
37	chr3:179045600-179053600	Strong transcription	Fetal Lung	lung
38	chr3:179045600-179053600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:179045600-179053600	Strong transcription	K562	blood
40	chr3:179045600-179054600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:179045600-179054800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:179045600-179054800	Strong transcription	Liver	Liver
43	chr3:179045600-179054800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr3:179045800-179053200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:179045800-179053400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:179045800-179054400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:179045800-179054600	Strong transcription	HUVEC	blood vessel
48	chr3:179045800-179054800	Strong transcription	Adipose Nuclei	Adipose
49	chr3:179045800-179055000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:179045800-179055600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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