Variant report

Variant	rs73822688
Chromosome Location	chr4:62449618-62449619
allele	A/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	TEAD4	chr4:62449493-62449744	ECC-1	luminal epithelium:	n/a	n/a
2	FOSL2	chr4:62449447-62449817	SK-N-SH	brain:	n/a	chr4:62449616-62449626 chr4:62449617-62449626 chr4:62449616-62449626
3	STAT3	chr4:62449562-62449773	MCF10A-Er-Src	breast:	n/a	chr4:62449617-62449626
4	STAT3	chr4:62449474-62449713	MCF10A-Er-Src	breast:	n/a	chr4:62449617-62449626
5	MAX	chr4:62449478-62449792	ECC-1	luminal epithelium:	n/a	n/a
6	MYC	chr4:62449551-62449791	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr4:62449383-62449848	MCF10A-Er-Src	breast:	n/a	chr4:62449616-62449626 chr4:62449617-62449626 chr4:62449616-62449626
8	JUND	chr4:62449433-62449704	HepG2	liver:	n/a	chr4:62449616-62449626 chr4:62449617-62449626 chr4:62449616-62449626
9	FOS	chr4:62449443-62449821	MCF10A-Er-Src	breast:	n/a	chr4:62449616-62449626 chr4:62449617-62449626 chr4:62449616-62449626
10	MYC	chr4:62449483-62449788	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr4:62449558-62449722	MCF10A-Er-Src	breast:	n/a	chr4:62449617-62449626
12	JUN	chr4:62449556-62449637	H1-hESC	embryonic stem cell:	n/a	chr4:62449616-62449626 chr4:62449617-62449626 chr4:62449616-62449626
13	STAT3	chr4:62449512-62449859	MCF10A-Er-Src	breast:	n/a	chr4:62449617-62449626
14	FOS	chr4:62449429-62449830	MCF10A-Er-Src	breast:	n/a	chr4:62449616-62449626 chr4:62449617-62449626 chr4:62449616-62449626
15	E2F4	chr4:62449493-62449883	MCF10A-Er-Src	breast:	n/a	n/a
16	TEAD4	chr4:62449370-62449813	ECC-1	luminal epithelium:	n/a	n/a
17	JUND	chr4:62449288-62449790	H1-hESC	embryonic stem cell:	n/a	chr4:62449616-62449626 chr4:62449617-62449626 chr4:62449616-62449626
18	FOS	chr4:62449287-62449899	MCF10A-Er-Src	breast:	n/a	chr4:62449616-62449626 chr4:62449617-62449626 chr4:62449616-62449626

Variant related genes	Relation type
LPHN3	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs2088113	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55636236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55773246	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55939610	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56338474	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59130415	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60655392	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73822609	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73822610	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73822617	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73822619	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73822621	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73822622	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73822651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73822652	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73822654	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73822690	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73822691	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73822692	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73822695	0.84[AMR][1000 genomes]
rs73825906	0.80[AMR][1000 genomes]
rs73825907	0.84[AMR][1000 genomes]
rs7660587	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9917973	0.83[EUR][1000 genomes]
rs9918049	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868844	chr4:62241702-62497248	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv461377	chr4:62368762-62883431	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv594328	chr4:62368762-62883431	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1004815	chr4:62398737-62553769	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv537110	chr4:62398737-62553769	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv594329	chr4:62416593-62478230	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv879077	chr4:62419426-62545435	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62446400-62462200	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:62449000-62450000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:62449000-62450200	Enhancers	NHEK	skin
4	chr4:62449200-62450200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:62449400-62450200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr4:62449400-62450200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr4:62449600-62450200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr4:62449600-62450200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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