Variant report

Variant	rs3018069
Chromosome Location	chr4:107291166-107291167
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	CTCF	chr4:107290397-107291168	HCT-116	colon:	n/a	chr4:107290804-107290813 chr4:107290803-107290816 chr4:107290800-107290818
2	RAD21	chr4:107290480-107291312	SK-N-SH	brain:	n/a	chr4:107290802-107290811 chr4:107290806-107290818 chr4:107290806-107290816 chr4:107291019-107291029
3	CTCF	chr4:107290539-107291170	SK-N-SH	brain:	n/a	chr4:107290804-107290813 chr4:107290803-107290816 chr4:107290800-107290818
4	RAD21	chr4:107290602-107291278	IMR90	lung:	n/a	chr4:107290802-107290811 chr4:107290806-107290818 chr4:107290806-107290816 chr4:107291019-107291029
5	CTCF	chr4:107290522-107291185	A549	lung:	n/a	chr4:107290804-107290813 chr4:107290803-107290816 chr4:107290800-107290818

No.	Distal block	Cell Line	Cell type
1	chr4:107290301..107292526-chr4:107422827..107424058,19	MCF-7	breast:
2	chr4:107290348..107291609-chr4:107422851..107424531,10	MCF-7	breast:
3	chr4:107290770..107291311-chr4:107424769..107425646,2	MCF-7	breast:

Variant related genes	Relation type
GIMD1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11732791	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11931386	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12642691	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12650692	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13101612	0.84[EUR][1000 genomes]
rs13113845	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13114479	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13121614	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13138528	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2691804	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2949625	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2949650	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3018066	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109953	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3109955	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3109958	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3109960	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3113249	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3113250	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3113252	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3133168	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3133169	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4374692	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4569824	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6533242	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6819081	0.84[EUR][1000 genomes]
rs7356287	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7668276	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7682646	0.81[EUR][1000 genomes]
rs7693448	0.90[AMR][1000 genomes];0.86[EUR][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	nsv830029	chr4:107203096-107353483	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1008963	chr4:107282656-107384924	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3018069	SCYE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107290000-107291200	Weak transcription	NHDF-Ad	bronchial
2	chr4:107290400-107291200	Enhancers	HUVEC	blood vessel
3	chr4:107290400-107291600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr4:107290600-107291200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:107290600-107291200	Enhancers	Rectal Smooth Muscle	rectum
6	chr4:107290600-107291200	Enhancers	Osteobl	bone
7	chr4:107290800-107291200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr4:107290800-107291200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:107290800-107291200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:107290800-107291200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:107290800-107291200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:107290800-107291200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:107290800-107291600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr4:107290800-107291600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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