Variant report

Variant	rs358717
Chromosome Location	chr3:155527287-155527288
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	GATA3	chr3:155526936-155527505	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr3:155526944-155527520	SK-N-SH	brain:	n/a	n/a
3	GATA2	chr3:155527044-155527385	HUVEC	blood vessel:	n/a	n/a
4	FOS	chr3:155526994-155527415	HUVEC	blood vessel:	n/a	chr3:155527096-155527105

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155522731..155527439-chr3:155568712..155573851,7	MCF-7	breast:
2	chr3:155525612..155527691-chr3:155537327..155538828,2	K562	blood:

Variant related genes	Relation type
C3orf33	TF binding region
ENSG00000169359	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs168586	1.00[ASW][hapmap];0.88[CEU][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs168587	0.87[ASN][1000 genomes]
rs35245064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs358715	0.85[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs358716	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs358718	0.81[CHB][hapmap];0.88[JPT][hapmap];0.99[ASN][1000 genomes]
rs389893	0.81[CHB][hapmap];0.88[JPT][hapmap];0.99[ASN][1000 genomes]
rs4434110	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6764439	0.81[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7637461	0.81[CHB][hapmap];0.88[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv999641	chr3:155481097-155534616	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	esv2753744	chr3:155487298-155707298	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs358717	SLC33A1	cis	cerebellum	SCAN
rs358717	SLC33A1	cis	parietal	SCAN
rs358717	PTX3	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155524400-155527400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:155524400-155542800	Weak transcription	Left Ventricle	heart
3	chr3:155524400-155543600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:155524400-155547000	Weak transcription	HSMMtube	muscle
5	chr3:155524400-155565800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:155524400-155567400	Weak transcription	Lung	lung
7	chr3:155524400-155569400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:155524600-155527400	Weak transcription	Osteobl	bone
9	chr3:155524600-155532800	Weak transcription	K562	blood
10	chr3:155524600-155544200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:155524600-155563400	Weak transcription	Brain Angular Gyrus	brain
12	chr3:155524600-155568000	Weak transcription	HUVEC	blood vessel
13	chr3:155526000-155543000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:155527000-155527400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:155527000-155527600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:155527200-155527400	Enhancers	NHDF-Ad	bronchial
17	chr3:155527200-155527600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr3:155527200-155527600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:155527200-155527600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:155527200-155527600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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