Variant report

Variant	rs4666383
Chromosome Location	chr2:20572094-20572095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20564625..20568805-chr2:20571129..20576493,6	MCF-7	breast:
2	chr2:20571196..20572728-chr2:20579213..20580832,2	MCF-7	breast:
3	chr2:20570098..20572702-chr2:20619357..20621600,2	MCF-7	breast:
4	chr2:20569349..20572195-chr2:20573816..20575777,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10190763	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11096655	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11679966	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11683916	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11686919	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2110409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2160072	0.88[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2348704	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs343163	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343164	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs343165	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771228	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs4666299	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4666304	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4666305	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4666382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6713329	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6754782	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6756819	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7355288	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7596797	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873716	chr2:20572094-20621404	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4666383	WDR35	cis	parietal	SCAN
rs4666383	HS1BP3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20565200-20578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:20565800-20575200	Weak transcription	NH-A	brain
3	chr2:20569600-20574200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:20570200-20574800	Weak transcription	Placenta	Placenta
5	chr2:20570200-20578600	Weak transcription	Ovary	ovary
6	chr2:20571600-20572200	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr2:20571600-20575000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:20571800-20572200	Enhancers	Fetal Brain Female	brain
9	chr2:20571800-20572800	Enhancers	Fetal Brain Male	brain
10	chr2:20571800-20576600	Weak transcription	Fetal Lung	lung

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