Variant report

Variant	rs59333548
Chromosome Location	chr3:179160155-179160156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:179151891..179154516-chr3:179158416..179160439,2	K562	blood:
2	chr3:179158232..179160460-chr3:179167836..179170470,2	K562	blood:
3	chr3:179143519..179146225-chr3:179157504..179160414,2	K562	blood:

Variant related genes	Relation type
ENSG00000114450	Chromatin interaction
ENSG00000239255	Chromatin interaction

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

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

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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13320472	0.81[AMR][1000 genomes]
rs16830445	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16830460	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28512433	1.00[AMR][1000 genomes]
rs28522651	0.89[AMR][1000 genomes]
rs55805052	0.89[AMR][1000 genomes]
rs56265474	1.00[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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59062224	0.89[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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61325843	0.89[AMR][1000 genomes]
rs6778235	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6800044	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808866	0.89[AMR][1000 genomes]
rs73043406	0.89[AMR][1000 genomes]
rs73043407	0.89[AMR][1000 genomes]
rs73043413	0.89[AMR][1000 genomes]
rs73045191	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73045195	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73045198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73059758	0.89[AMR][1000 genomes]
rs73059766	0.89[AMR][1000 genomes]
rs7355835	1.00[AMR][1000 genomes]
rs73883508	1.00[AMR][1000 genomes]
rs73883509	1.00[AMR][1000 genomes]
rs73886620	0.89[AMR][1000 genomes]
rs7611533	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7618506	0.93[AFR][1000 genomes]
rs7625719	0.89[AMR][1000 genomes]
rs9814990	1.00[AMR][1000 genomes]
rs9815687	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9829054	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9834493	1.00[AMR][1000 genomes]
rs9861354	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9864857	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9872939	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9879952	1.00[EUR][1000 genomes]
rs9884070	1.00[AMR][1000 genomes];1.00[EUR][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:11 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179084000-179167200	Weak transcription	Fetal Brain Male	brain
2	chr3:179112000-179167200	Weak transcription	Fetal Kidney	kidney
3	chr3:179132800-179167000	Weak transcription	Hela-S3	cervix
4	chr3:179143000-179163800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:179143200-179166800	Weak transcription	HSMM	muscle
6	chr3:179143200-179167000	Weak transcription	HSMMtube	muscle
7	chr3:179143200-179167200	Weak transcription	Fetal Brain Female	brain
8	chr3:179143200-179168200	Weak transcription	Esophagus	oesophagus
9	chr3:179143400-179165600	Weak transcription	Fetal Intestine Small	intestine
10	chr3:179143400-179167000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:179143600-179166800	Weak transcription	Brain Germinal Matrix	brain
12	chr3:179143800-179167000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:179148000-179164400	Weak transcription	Fetal Heart	heart
14	chr3:179148400-179162200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:179150000-179162400	Weak transcription	Aorta	Aorta
16	chr3:179150000-179164000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:179150600-179161800	Weak transcription	NHEK	skin
18	chr3:179150800-179164400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:179150800-179166200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:179150800-179166800	Weak transcription	Fetal Lung	lung
21	chr3:179150800-179167600	Weak transcription	Placenta	Placenta
22	chr3:179151200-179160400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:179151200-179161800	Weak transcription	Osteobl	bone
24	chr3:179151400-179161800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:179151400-179165000	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:179151400-179166800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:179151600-179165600	Weak transcription	NHDF-Ad	bronchial
28	chr3:179151800-179162200	Weak transcription	NH-A	brain
29	chr3:179152000-179163800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:179152000-179165600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:179152000-179166800	Weak transcription	NHLF	lung
32	chr3:179152400-179162200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:179152400-179166600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:179152600-179165000	Weak transcription	Right Atrium	heart
35	chr3:179152800-179168600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:179154000-179161000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:179155000-179166600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:179156800-179160200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:179156800-179164400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:179156800-179164600	Weak transcription	Lung	lung
41	chr3:179157000-179163600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:179157000-179163800	Weak transcription	Dnd41	blood
43	chr3:179157000-179164200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:179157000-179165000	Weak transcription	Fetal Thymus	thymus
45	chr3:179157200-179162200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:179157200-179166600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:179157400-179160400	Weak transcription	HUVEC	blood vessel
48	chr3:179157400-179163400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:179157400-179163800	Weak transcription	Spleen	Spleen
50	chr3:179157400-179164600	Weak transcription	Fetal Stomach	stomach

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