Variant report

Variant	rs28647422
Chromosome Location	chr4:3410559-3410560
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	POLR2A	chr4:3410557-3410769	HepG2	liver:	n/a	n/a
2	HEY1	chr4:3410409-3410657	HepG2	liver:	n/a	n/a
3	KAP1	chr4:3410135-3410898	U2OS	brain:	n/a	chr4:3410481-3410489
4	MAFK	chr4:3410404-3410786	HepG2	liver:	n/a	chr4:3410604-3410620 chr4:3410604-3410619
5	MXI1	chr4:3409680-3410847	HepG2	liver:	n/a	chr4:3410015-3410024 chr4:3410366-3410375
6	TBP	chr4:3409732-3410720	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:3410341-3411099	SK-N-MC	brain:	n/a	n/a
8	ZNF263	chr4:3410425-3411030	HEK293-T-REx	kidney:	n/a	n/a
9	KAP1	chr4:3410179-3410936	HEK293	kidney:	n/a	chr4:3410481-3410489
10	MAFF	chr4:3409748-3410798	HepG2	liver:	n/a	chr4:3410603-3410621
11	POLR2A	chr4:3409049-3411706	HepG2	liver:	n/a	n/a
12	E2F4	chr4:3410559-3410662	MCF10A-Er-Src	breast:	n/a	n/a
13	MAFK	chr4:3410489-3410738	IMR90	lung:	n/a	chr4:3410604-3410620 chr4:3410604-3410619
14	MAFK	chr4:3409778-3410792	HepG2	liver:	n/a	chr4:3410604-3410620 chr4:3410604-3410619
15	MAFF	chr4:3410489-3410665	K562	blood:	n/a	chr4:3410603-3410621
16	POLR2A	chr4:3410171-3411208	SK-N-MC	brain:	n/a	n/a
17	MAX	chr4:3409575-3410584	HepG2	liver:	n/a	chr4:3409826-3409833 chr4:3409826-3409842 chr4:3409823-3409834 chr4:3410366-3410373 chr4:3409825-3409834 chr4:3410365-3410375 chr4:3410364-3410375
18	MAX	chr4:3409557-3410947	HepG2	liver:	n/a	chr4:3409826-3409833 chr4:3410915-3410926 chr4:3409826-3409842 chr4:3409823-3409834 chr4:3410366-3410373 chr4:3409825-3409834 chr4:3410365-3410375 chr4:3410364-3410375
19	FOXP2	chr4:3410296-3411128	SK-N-MC	brain:	n/a	n/a
20	MAFK	chr4:3410492-3410705	K562	blood:	n/a	chr4:3410604-3410620 chr4:3410604-3410619
21	POLR2A	chr4:3409851-3410730	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:3406805..3408629-chr4:3410339..3412435,2	K562	blood:
2	chr4:3406805..3408951-chr4:3410339..3412691,4	K562	blood:
3	chr4:3406020..3409060-chr4:3409892..3412921,3	MCF-7	breast:

Variant related genes	Relation type
RGS12	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10007038	0.82[AFR][1000 genomes]
rs10035011	0.82[AFR][1000 genomes]
rs13435851	0.82[AFR][1000 genomes]
rs1406673	0.80[AFR][1000 genomes]
rs28410709	0.82[AFR][1000 genomes]
rs61527677	0.82[AFR][1000 genomes]
rs6446736	0.82[AFR][1000 genomes]
rs6446737	0.82[AFR][1000 genomes]
rs6446738	0.82[AFR][1000 genomes]
rs6446739	0.82[AFR][1000 genomes]
rs6812029	0.82[AFR][1000 genomes]
rs6829410	0.80[AFR][1000 genomes]
rs73792009	0.82[AFR][1000 genomes]
rs73792031	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3390000-3417200	Weak transcription	Gastric	stomach
2	chr4:3391000-3414000	Weak transcription	Primary T cells from cord blood	blood
3	chr4:3391800-3424200	Weak transcription	Colonic Mucosa	Colon
4	chr4:3392000-3417200	Weak transcription	Pancreas	Pancrea
5	chr4:3399200-3432200	Weak transcription	Right Atrium	heart
6	chr4:3401600-3416200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:3401800-3416000	Weak transcription	Right Ventricle	heart
8	chr4:3403400-3417200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:3404800-3414200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:3405000-3410800	Strong transcription	Esophagus	oesophagus
11	chr4:3405000-3415000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:3405200-3415800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:3405200-3418800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:3406400-3417200	Weak transcription	HMEC	breast
15	chr4:3406600-3413800	Weak transcription	Adipose Nuclei	Adipose
16	chr4:3406600-3417200	Weak transcription	HSMM	muscle
17	chr4:3406800-3415600	Weak transcription	Lung	lung
18	chr4:3406800-3417400	Weak transcription	Aorta	Aorta
19	chr4:3407200-3410600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:3407200-3417200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:3407200-3417200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr4:3407200-3417800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:3407400-3415400	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:3407400-3417800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:3407600-3415400	Weak transcription	Fetal Heart	heart
26	chr4:3407600-3417200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:3407600-3418000	Weak transcription	Left Ventricle	heart
28	chr4:3407800-3417600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:3408200-3414000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr4:3408200-3416600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:3408600-3417200	Weak transcription	HSMMtube	muscle
32	chr4:3408800-3411600	Enhancers	Ovary	ovary
33	chr4:3408800-3436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:3409000-3411800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr4:3409000-3412400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:3409000-3415000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:3409000-3415200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:3409200-3410800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:3409200-3411000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:3409200-3411200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:3409200-3412800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:3409400-3410600	Weak transcription	Brain Anterior Caudate	brain
43	chr4:3409400-3410600	Weak transcription	Fetal Brain Male	brain
44	chr4:3409400-3411000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:3409400-3417200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:3409600-3410600	Flanking Active TSS	Liver	Liver
47	chr4:3409600-3410800	Flanking Active TSS	HepG2	liver
48	chr4:3409600-3412000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:3409600-3415400	Weak transcription	Fetal Lung	lung
50	chr4:3409800-3411000	Genic enhancers	Fetal Intestine Small	intestine

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