Variant report

Variant	rs1012388
Chromosome Location	chr17:38872625-38872626
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38800758..38806200-chr17:38867662..38875106,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073584	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11078950	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11650910	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1526601	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1961204	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2011870	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2272288	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429547	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2429548	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2429550	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2429551	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2462957	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2462960	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2462961	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462965	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2462966	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462967	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2462969	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2469817	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2469819	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2469820	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2469825	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs723728	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs723729	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs726849	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758630	0.93[AFR][1000 genomes]
rs8065040	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs874889	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs887376	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9303294	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9675112	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1012388	SMARCE1	cis	multi-tissue	Pritchard
rs1012388	KRT24	cis	Esophagus Mucosa	GTEx
rs1012388	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs1012388	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38854000-38875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:38860000-38890200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:38864800-38874800	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links