Variant report

Variant	rs58643792
Chromosome Location	chr4:3011848-3011849
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2938205..2940461-chr4:3011705..3013436,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11935128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11947255	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34854780	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35248769	1.00[AMR][1000 genomes]
rs35492582	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35970030	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41264719	1.00[AMR][1000 genomes]
rs56733257	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57294059	1.00[AMR][1000 genomes]
rs57447128	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57779369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57812385	1.00[AMR][1000 genomes]
rs58036497	1.00[AMR][1000 genomes]
rs58202885	1.00[AMR][1000 genomes]
rs58376060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58782413	1.00[AMR][1000 genomes]
rs58966302	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58998372	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6812433	0.81[AFR][1000 genomes]
rs6813002	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6813023	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6826590	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6832730	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6845680	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73073038	1.00[AMR][1000 genomes]
rs73073070	1.00[AMR][1000 genomes]
rs73074803	1.00[AMR][1000 genomes]
rs73084106	0.90[AFR][1000 genomes]
rs73084115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73086132	1.00[AMR][1000 genomes]
rs73088165	1.00[AMR][1000 genomes]
rs7696059	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv1008436	chr4:2947160-3031195	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv536998	chr4:2947160-3031195	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv593438	chr4:2948456-3030097	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1008527	chr4:2957814-3019042	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv878453	chr4:2963222-3021383	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1008781	chr4:2964080-3019042	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1014675	chr4:2968222-3012723	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv998311	chr4:2981615-3012723	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv870141	chr4:2982146-3021346	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2979600-3025000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:2983600-3032000	Weak transcription	Fetal Brain Female	brain
3	chr4:2991400-3024600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr4:3003800-3024600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:3005000-3018600	Weak transcription	Left Ventricle	heart
6	chr4:3005800-3038600	Weak transcription	Right Ventricle	heart
7	chr4:3007000-3020600	Weak transcription	Brain Germinal Matrix	brain
8	chr4:3007200-3015200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:3007600-3024600	Weak transcription	Brain Angular Gyrus	brain
10	chr4:3008000-3013200	Weak transcription	Esophagus	oesophagus
11	chr4:3010600-3012800	Enhancers	HepG2	liver
12	chr4:3010600-3013400	Enhancers	HMEC	breast
13	chr4:3010800-3013200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:3011200-3012400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:3011200-3012400	Enhancers	NHDF-Ad	bronchial
16	chr4:3011200-3013400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:3011200-3013800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:3011200-3013800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:3011200-3013800	Enhancers	Hela-S3	cervix
20	chr4:3011200-3014400	Enhancers	Stomach Mucosa	stomach
21	chr4:3011400-3012400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:3011600-3012400	Weak transcription	Pancreas	Pancrea
23	chr4:3011600-3012600	Enhancers	GM12878-XiMat	blood
24	chr4:3011600-3012800	Weak transcription	Fetal Intestine Small	intestine
25	chr4:3011600-3013800	Enhancers	Fetal Lung	lung
26	chr4:3011800-3012200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:3011800-3013400	Enhancers	NHEK	skin
28	chr4:3011800-3039600	Weak transcription	Right Atrium	heart

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