Variant report

Variant	rs28489501
Chromosome Location	chr4:3414548-3414549
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr4:3414426-3414697	GM12878	blood:	n/a	chr4:3414506-3414524

Variant related genes	Relation type
RGS12	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10007038	0.91[AFR][1000 genomes]
rs10035011	0.91[AFR][1000 genomes]
rs10049879	0.81[AFR][1000 genomes]
rs13435851	0.91[AFR][1000 genomes]
rs1406673	0.89[AFR][1000 genomes]
rs16844254	0.85[AFR][1000 genomes]
rs16844260	0.85[AFR][1000 genomes]
rs16844272	0.84[AFR][1000 genomes]
rs28410709	0.91[AFR][1000 genomes]
rs28420539	0.85[AFR][1000 genomes]
rs28457232	0.87[AFR][1000 genomes]
rs28505211	0.96[AFR][1000 genomes]
rs28535968	0.85[AFR][1000 genomes]
rs28636983	0.88[AFR][1000 genomes]
rs58249502	0.85[AFR][1000 genomes]
rs61527677	0.91[AFR][1000 genomes]
rs6446736	0.91[AFR][1000 genomes]
rs6446737	0.91[AFR][1000 genomes]
rs6446738	0.91[AFR][1000 genomes]
rs6446739	0.91[AFR][1000 genomes]
rs6812029	0.91[AFR][1000 genomes]
rs6825183	0.88[AFR][1000 genomes]
rs6829410	0.89[AFR][1000 genomes]
rs6847900	0.85[AFR][1000 genomes]
rs73792009	0.91[AFR][1000 genomes]
rs73792011	0.88[AFR][1000 genomes]
rs73792031	0.91[AFR][1000 genomes]
rs73792038	0.99[AFR][1000 genomes]
rs73792070	0.84[AFR][1000 genomes]
rs7656119	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	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
4	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
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv933265	chr4:3392824-4283640	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
11	esv2757918	chr4:3394344-4350986	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
12	esv2759219	chr4:3394344-4350986	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
13	nsv461166	chr4:3405165-3451109	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv593450	chr4:3405165-3451109	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv878464	chr4:3405165-3505448	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv878465	chr4:3405165-3566567	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	esv1791851	chr4:3407753-3534022	Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
18	nsv1000383	chr4:3412585-3839781	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
19	nsv461167	chr4:3413209-3446112	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv593451	chr4:3413209-3446112	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv461168	chr4:3413209-3449652	Genic enhancers Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv593452	chr4:3413209-3449652	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv878466	chr4:3413209-3451109	Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv878467	chr4:3413209-3454304	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv878468	chr4:3413209-3471754	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
26	nsv878469	chr4:3413209-3566567	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
27	nsv878470	chr4:3413209-3566567	Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
28	nsv878471	chr4:3413209-3884998	Bivalent Enhancer Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3390000-3417200	Weak transcription	Gastric	stomach
2	chr4:3391800-3424200	Weak transcription	Colonic Mucosa	Colon
3	chr4:3392000-3417200	Weak transcription	Pancreas	Pancrea
4	chr4:3399200-3432200	Weak transcription	Right Atrium	heart
5	chr4:3401600-3416200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:3401800-3416000	Weak transcription	Right Ventricle	heart
7	chr4:3403400-3417200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:3405000-3415000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:3405200-3415800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:3405200-3418800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:3406400-3417200	Weak transcription	HMEC	breast
12	chr4:3406600-3417200	Weak transcription	HSMM	muscle
13	chr4:3406800-3415600	Weak transcription	Lung	lung
14	chr4:3406800-3417400	Weak transcription	Aorta	Aorta
15	chr4:3407200-3417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:3407200-3417200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr4:3407200-3417800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:3407400-3415400	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:3407400-3417800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:3407600-3415400	Weak transcription	Fetal Heart	heart
21	chr4:3407600-3417200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:3407600-3418000	Weak transcription	Left Ventricle	heart
23	chr4:3407800-3417600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:3408200-3416600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr4:3408600-3417200	Weak transcription	HSMMtube	muscle
26	chr4:3408800-3436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:3409000-3415000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:3409000-3415200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:3409400-3417200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:3409600-3415400	Weak transcription	Fetal Lung	lung
31	chr4:3410400-3415800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:3411000-3415200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:3411000-3415800	Weak transcription	Fetal Intestine Large	intestine
34	chr4:3411000-3416600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr4:3411000-3417800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:3411000-3436400	Strong transcription	Fetal Intestine Small	intestine
37	chr4:3411200-3436400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr4:3411200-3436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:3411400-3425600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:3411600-3415200	Weak transcription	Ovary	ovary
41	chr4:3411800-3420000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:3412000-3417200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:3412200-3415600	Weak transcription	HepG2	liver
44	chr4:3412200-3415800	Weak transcription	Spleen	Spleen
45	chr4:3412400-3416000	Weak transcription	Placenta	Placenta
46	chr4:3412400-3417600	Weak transcription	NHEK	skin
47	chr4:3412600-3415000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:3412600-3415200	Weak transcription	Fetal Brain Male	brain
49	chr4:3412600-3416200	Weak transcription	Liver	Liver
50	chr4:3412600-3417800	Weak transcription	Fetal Brain Female	brain

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