Variant report

Variant	rs60642432
Chromosome Location	chr4:77356015-77356016
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:77355949-77356504	ECC-1	luminal epithelium:	n/a	n/a
2	TEAD4	chr4:77355839-77356521	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr4:77355706-77356712	ECC-1	luminal epithelium:	n/a	chr4:77356583-77356597 chr4:77356514-77356528
4	NFIC	chr4:77355735-77356748	ECC-1	luminal epithelium:	n/a	chr4:77356209-77356226 chr4:77356209-77356225
5	STAT3	chr4:77355968-77356438	MCF10A-Er-Src	breast:	n/a	n/a
6	MAX	chr4:77355856-77356530	ECC-1	luminal epithelium:	n/a	n/a
7	TEAD4	chr4:77355911-77356415	ECC-1	luminal epithelium:	n/a	n/a
8	STAT3	chr4:77355951-77356369	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr4:77355929-77356499	PFSK-1	brain:	n/a	n/a
10	STAT3	chr4:77355990-77356371	MCF10A-Er-Src	breast:	n/a	n/a
11	E2F4	chr4:77355965-77356245	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr4:77355936-77356369	MCF10A-Er-Src	breast:	n/a	n/a
13	NFIC	chr4:77355824-77356548	ECC-1	luminal epithelium:	n/a	chr4:77356209-77356226 chr4:77356209-77356225
14	SMC3	chr4:77356006-77356400	Hela-S3	cervix:	n/a	n/a
15	FOS	chr4:77355956-77356299	MCF10A-Er-Src	breast:	n/a	n/a
16	FOXM1	chr4:77355718-77356605	ECC-1	luminal epithelium:	n/a	n/a
17	ZNF384	chr4:77356015-77356062	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:77356008-77356058	Caco-2	colon:	n/a
2	chr4:77356008-77356058	SK-N-SH	brain:	n/a
3	chr4:77356008-77356058	HPAEpiC	pulmonary alveolar:	n/a
4	chr4:77356008-77356058	CMK	blood:	n/a
5	chr4:77356008-77356058	NHDF-neo	bronchial:	n/a
6	chr4:77356008-77356058	A549	lung:	n/a
7	chr4:77356008-77356058	HUVEC	blood vessel:	n/a
8	chr4:77356008-77356058	SAEC	small airway:	n/a
9	chr4:77356008-77356058	AG04450	lung:	fetal
10	chr4:77356008-77356058	PFSK-1	brain:	n/a
11	chr4:77356008-77356058	AoSMC	blood vessel:	n/a
12	chr4:77356008-77356058	GM06990	blood:	n/a
13	chr4:77356008-77356058	AG09319	gingival:	n/a
14	chr4:77356008-77356058	SKMC	muscle:	n/a
15	chr4:77356008-77356058	AG09309	skin:	n/a
16	chr4:77356008-77356058	BJ	skin:	n/a
17	chr4:77356008-77356058	PrEC	prostate:	n/a
18	chr4:77356008-77356058	HRPEpiC	eye:	n/a
19	chr4:77356008-77356058	HCM	heart:	n/a
20	chr4:77356008-77356058	RPTEC	kidney:	n/a
21	chr4:77356008-77356058	AG04449	skin:	fetal
22	chr4:77356008-77356058	Hepatocyte	liver:	n/a
23	chr4:77356008-77356058	HIPEpiC	eye:	n/a
24	chr4:77356008-77356058	HCF	heart:	n/a
25	chr4:77356008-77356058	NB4	blood:	n/a
26	chr4:77356008-77356058	MCF-7	breast:	n/a
27	chr4:77356008-77356058	MCF10A-Er-Src	breast:	n/a
28	chr4:77356008-77356058	ECC-1	luminal epithelium:	n/a
29	chr4:77356008-77356058	LNCaP	prostate:	n/a
30	chr4:77356008-77356058	ovcar-3	ovarian:	n/a
31	chr4:77356008-77356058	PANC-1	pancreas:	n/a
32	chr4:77356008-77356058	NT2-D1	testis:	n/a
33	chr4:77356008-77356058	HRE	kidney:	n/a
34	chr4:77356008-77356058	GM12892	blood:	n/a
35	chr4:77356008-77356058	Hela-S3	cervix:	n/a
36	chr4:77356008-77356058	GM19239	blood:	n/a
37	chr4:77356008-77356058	HepG2	liver:	n/a
38	chr4:77356008-77356058	GM12878	blood:	n/a
39	chr4:77356008-77356058	H1-hESC	embryonic stem cell:	embryo
40	chr4:77356008-77356058	HNPCEpiC	eye:	n/a
41	chr4:77356008-77356058	HL-60	blood:	n/a
42	chr4:77356008-77356058	Jurkat	blood:	n/a
43	chr4:77356008-77356058	HMEC	breast:	n/a
44	chr4:77356008-77356058	NH-A	brain:	n/a
45	chr4:77356008-77356058	HRCEpiC	kidney:	n/a
46	chr4:77356008-77356058	AG10803	skin:	n/a
47	chr4:77356008-77356058	ProgFib	skin:	n/a
48	chr4:77356008-77356058	HEK293	kidney:	embryo
49	chr4:77356008-77356058	GM12891	blood:	n/a
50	chr4:77356008-77356058	NHBE	bronchial:	n/a

No data

Variant related genes	Relation type
SHROOM3	TF binding region
SHROOM3	CpG island

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs57758833	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58661348	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58772873	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6827818	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757941	chr4:77264596-77417457	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759262	chr4:77264596-77455405	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77344000-77356200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:77352000-77356200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:77352000-77356200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:77352000-77356200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:77352200-77356200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:77353800-77357000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:77354200-77356200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr4:77354400-77356200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:77354600-77356200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr4:77355200-77356200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:77355400-77356200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:77355400-77358800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:77355600-77356400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr4:77355600-77356400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr4:77355800-77356200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:77355800-77356400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:77355800-77356400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr4:77355800-77356600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:77355800-77356600	Enhancers	Stomach Mucosa	stomach
20	chr4:77355800-77356800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:77356000-77356200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:77356000-77356200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:77356000-77356200	Flanking Active TSS	Liver	Liver
24	chr4:77356000-77356200	Flanking Active TSS	Fetal Heart	heart
25	chr4:77356000-77356200	Enhancers	Fetal Intestine Large	intestine
26	chr4:77356000-77356200	Enhancers	NH-A	brain
27	chr4:77356000-77356400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr4:77356000-77356400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr4:77356000-77356400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr4:77356000-77356400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr4:77356000-77356400	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr4:77356000-77356400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr4:77356000-77356400	Enhancers	Fetal Lung	lung
34	chr4:77356000-77356400	Flanking Active TSS	Hela-S3	cervix
35	chr4:77356000-77356600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:77356000-77356600	Enhancers	NHEK	skin
37	chr4:77356000-77357000	Active TSS	Aorta	Aorta
38	chr4:77356000-77357400	Active TSS	Fetal Muscle Trunk	muscle
39	chr4:77356000-77357400	Flanking Active TSS	HMEC	breast
40	chr4:77356000-77358600	Active TSS	Right Atrium	heart
41	chr4:77356000-77359000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:77356000-77359200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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