Variant report

Variant	rs554642261
Chromosome Location	chr4:53524670-53524671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:53524490-53524777	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:53523695-53524727	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD1	chr4:53524442-53524929	H1-hESC	embryonic stem cell:	n/a	n/a
4	WRNIP1	chr4:53524441-53524925	GM12878	blood:	n/a	n/a
5	MXI1	chr4:53523572-53526602	IMR90	lung:	n/a	n/a
6	RUNX3	chr4:53524646-53525711	GM12878	blood:	n/a	n/a
7	MAZ	chr4:53524556-53526814	IMR90	lung:	n/a	chr4:53525015-53525025
8	SIN3A	chr4:53523707-53526506	H1-hESC	embryonic stem cell:	n/a	chr4:53526089-53526102 chr4:53525406-53525417 chr4:53525373-53525383
9	POLR2A	chr4:53523759-53526466	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr4:53523819-53524671	H1-hESC	embryonic stem cell:	n/a	chr4:53524291-53524300
11	USF2	chr4:53524531-53524694	Hela-S3	cervix:	n/a	n/a
12	MYC	chr4:53524631-53524823	K562	blood:	n/a	n/a
13	ZNF143	chr4:53523989-53524724	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:53523849..53530507-chr4:53576531..53584814,17	K562	blood:
2	chr4:53524001..53527558-chr4:53577308..53580194,4	MCF-7	breast:
3	chr4:53519355..53522911-chr4:53523707..53526726,6	MCF-7	breast:
4	chr4:53523914..53526614-chr4:53586643..53588754,3	MCF-7	breast:
5	chr4:53492777..53495734-chr4:53523846..53526517,2	K562	blood:
6	chr4:53523968..53528771-chr4:53576572..53580241,9	MCF-7	breast:
7	chr4:53522789..53525024-chr4:53586830..53589438,2	K562	blood:
8	chr4:53515781..53522890-chr4:53523068..53527068,15	MCF-7	breast:
9	chr4:53522503..53529252-chr4:53576629..53581800,10	K562	blood:

No data

Variant related genes	Relation type
USP46-AS1	TF binding region
USP46	TF binding region
ENSG00000212588	Chromatin interaction
ENSG00000264585	Chromatin interaction
ENSG00000109189	Chromatin interaction
ENSG00000226950	Chromatin interaction
ENSG00000248375	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2754049	chr4:53454272-53539672	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv524494	chr4:53459620-53582065	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	esv3344129	chr4:53524220-53527168	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53518600-53525200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr4:53523000-53527000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:53523600-53524800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:53523600-53524800	Enhancers	Primary B cells from peripheral blood	blood
5	chr4:53523600-53524800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:53523600-53524800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:53523600-53524800	Flanking Active TSS	Right Ventricle	heart
8	chr4:53523600-53524800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr4:53523600-53524800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr4:53523600-53525000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
11	chr4:53523600-53526400	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr4:53523800-53524800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr4:53523800-53524800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:53523800-53524800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:53523800-53524800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr4:53523800-53524800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:53523800-53524800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:53523800-53524800	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr4:53523800-53524800	Flanking Active TSS	Fetal Brain Female	brain
20	chr4:53523800-53524800	Flanking Active TSS	Fetal Muscle Trunk	muscle
21	chr4:53523800-53524800	Flanking Active TSS	Left Ventricle	heart
22	chr4:53523800-53525000	Flanking Active TSS	Brain Hippocampus Middle	brain
23	chr4:53523800-53525000	Flanking Active TSS	Fetal Muscle Leg	muscle
24	chr4:53523800-53525000	Flanking Active TSS	HepG2	liver
25	chr4:53523800-53526200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr4:53523800-53526400	Active TSS	Brain Angular Gyrus	brain
27	chr4:53523800-53526600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr4:53523800-53526600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:53523800-53526600	Active TSS	NHLF	lung
30	chr4:53523800-53526800	Active TSS	NHDF-Ad	bronchial
31	chr4:53523800-53527200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:53524000-53524800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:53524000-53524800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr4:53524000-53524800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:53524000-53524800	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr4:53524000-53524800	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr4:53524000-53524800	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr4:53524000-53524800	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr4:53524000-53524800	Flanking Active TSS	Fetal Lung	lung
40	chr4:53524000-53524800	Flanking Active TSS	Placenta	Placenta
41	chr4:53524000-53524800	Flanking Active TSS	Pancreas	Pancrea
42	chr4:53524000-53524800	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr4:53524000-53524800	Enhancers	Spleen	Spleen
44	chr4:53524000-53524800	Flanking Active TSS	GM12878-XiMat	blood
45	chr4:53524000-53524800	Flanking Active TSS	NHEK	skin
46	chr4:53524000-53525000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr4:53524000-53525000	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr4:53524000-53525000	Flanking Active TSS	Dnd41	blood
49	chr4:53524000-53526200	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr4:53524000-53526200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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