Variant report

Variant	rs168586
Chromosome Location	chr3:155527495-155527496
allele	A/G
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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155525612..155527691-chr3:155537327..155538828,2	K562	blood:
2	chr3:155527339..155529123-chr3:155547741..155549452,2	K562	blood:

Variant related genes	Relation type
C3orf33	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs168587	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs35245064	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs358715	0.81[CEU][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs358716	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs358717	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]
rs358718	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs389893	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4434110	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6764439	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs7637461	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs168586	SLC33A1	cis	cerebellum	SCAN
rs168586	SLC33A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155524400-155542800	Weak transcription	Left Ventricle	heart
2	chr3:155524400-155543600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:155524400-155547000	Weak transcription	HSMMtube	muscle
4	chr3:155524400-155565800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:155524400-155567400	Weak transcription	Lung	lung
6	chr3:155524400-155569400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:155524600-155532800	Weak transcription	K562	blood
8	chr3:155524600-155544200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:155524600-155563400	Weak transcription	Brain Angular Gyrus	brain
10	chr3:155524600-155568000	Weak transcription	HUVEC	blood vessel
11	chr3:155526000-155543000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:155527000-155527600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:155527200-155527600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:155527200-155527600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:155527200-155527600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:155527200-155527600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:155527400-155527600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr3:155527400-155527600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:155527400-155527600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:155527400-155543200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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