Variant report

Variant	rs2488807
Chromosome Location	chr4:3020131-3020132
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3018174..3020702-chr4:3033149..3035884,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13111546	0.86[EUR][1000 genomes]
rs2471329	0.93[AMR][1000 genomes]
rs2488810	0.81[AMR][1000 genomes]
rs2515930	0.93[AMR][1000 genomes]
rs2515931	0.93[AMR][1000 genomes]
rs28707127	1.00[EUR][1000 genomes]
rs2960309	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3021125	0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
9	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
10	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:22 , 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	chr4:3005800-3038600	Weak transcription	Right Ventricle	heart
6	chr4:3007000-3020600	Weak transcription	Brain Germinal Matrix	brain
7	chr4:3007600-3024600	Weak transcription	Brain Angular Gyrus	brain
8	chr4:3011800-3039600	Weak transcription	Right Atrium	heart
9	chr4:3012800-3024800	Weak transcription	Aorta	Aorta
10	chr4:3013200-3022600	Weak transcription	Ovary	ovary
11	chr4:3013400-3022200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:3013800-3022600	Weak transcription	Adipose Nuclei	Adipose
13	chr4:3014600-3026200	Weak transcription	Fetal Brain Male	brain
14	chr4:3014800-3025000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:3016000-3020600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:3016200-3033200	Weak transcription	Pancreas	Pancrea
17	chr4:3017000-3020600	Weak transcription	GM12878-XiMat	blood
18	chr4:3017800-3022800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:3019000-3022800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:3019200-3039000	Weak transcription	Left Ventricle	heart
21	chr4:3019800-3024600	Weak transcription	HSMMtube	muscle
22	chr4:3020000-3021600	Enhancers	Cortex derived primary cultured neurospheres	brain

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