Variant report

Variant	rs3025799
Chromosome Location	chr4:3259596-3259597
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	chr4:3243567..3245468-chr4:3259325..3261175,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10000252	1.00[AFR][1000 genomes]
rs10011127	1.00[AFR][1000 genomes]
rs10011241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10030079	1.00[AFR][1000 genomes]
rs28376014	0.85[AMR][1000 genomes]
rs28728173	0.85[AMR][1000 genomes]
rs3025836	1.00[AFR][1000 genomes]
rs363138	1.00[AFR][1000 genomes]
rs9995687	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active 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	11 gene(s)	inside rSNPs	diseases
4	nsv524211	chr4:3215835-3270488	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv470003	chr4:3215835-3275484	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
8	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv878457	chr4:3231661-3278517	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
12	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3238200-3261400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:3238600-3259800	Weak transcription	NH-A	brain
4	chr4:3243000-3260000	Weak transcription	Brain Angular Gyrus	brain
5	chr4:3243400-3259600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:3244800-3259600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:3245200-3259800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:3245200-3260000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:3246400-3261000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:3246600-3261400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:3247200-3261000	Weak transcription	Aorta	Aorta
12	chr4:3247600-3268400	Weak transcription	Primary T cells from cord blood	blood
13	chr4:3248200-3259600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:3248800-3260800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:3249600-3260000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:3251000-3262600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:3252400-3265200	Weak transcription	Fetal Lung	lung
18	chr4:3252400-3271400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:3253000-3262800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:3253200-3259600	Weak transcription	Fetal Intestine Large	intestine
21	chr4:3253200-3262200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:3253400-3260400	Strong transcription	Fetal Stomach	stomach
23	chr4:3255600-3260600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:3255800-3271000	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:3256400-3259800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:3257000-3260000	Strong transcription	Spleen	Spleen
27	chr4:3257000-3271800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:3257400-3259600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr4:3257400-3259600	Strong transcription	Gastric	stomach
30	chr4:3257400-3260000	Strong transcription	Pancreas	Pancrea
31	chr4:3257400-3260200	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr4:3257600-3259600	Strong transcription	Brain Germinal Matrix	brain
33	chr4:3258000-3259600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:3258200-3259800	Weak transcription	Liver	Liver
35	chr4:3258200-3260000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr4:3258400-3259800	Enhancers	Fetal Muscle Leg	muscle
37	chr4:3258400-3260000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:3258400-3271000	Weak transcription	Brain Anterior Caudate	brain
39	chr4:3258400-3271000	Weak transcription	Right Ventricle	heart
40	chr4:3258400-3271000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr4:3258600-3260000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr4:3258600-3260400	Weak transcription	Adipose Nuclei	Adipose
43	chr4:3258600-3269600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:3258800-3260400	Enhancers	HSMM	muscle
45	chr4:3258800-3260600	Enhancers	Primary B cells from peripheral blood	blood
46	chr4:3259200-3259800	Enhancers	HSMMtube	muscle
47	chr4:3259200-3260200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:3259200-3269600	Weak transcription	Fetal Intestine Small	intestine
49	chr4:3259200-3270000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr4:3259400-3259600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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