Variant report

Variant	rs4858069
Chromosome Location	chr3:23384779-23384780
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23375136..23376980-chr3:23383143..23385276,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11708160	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11711072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11715841	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs11717397	0.82[AFR][1000 genomes]
rs12386394	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12715046	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12715048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13074192	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs13087861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1353322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1692617	0.83[GIH][hapmap]
rs1692622	0.82[JPT][hapmap]
rs1874235	0.84[YRI][hapmap]
rs2055310	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs2133331	0.89[CEU][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs2173460	0.89[CEU][hapmap]
rs2359759	0.85[GIH][hapmap];0.84[MKK][hapmap]
rs2884731	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3104243	0.83[GIH][hapmap]
rs3111311	0.89[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3817002	0.89[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4241512	0.87[AFR][1000 genomes]
rs4858074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858504	0.84[YRI][hapmap]
rs4858505	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858509	0.92[EUR][1000 genomes]
rs4858510	0.84[AMR][1000 genomes]
rs55797660	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58748418	0.81[EUR][1000 genomes]
rs60430884	0.82[EUR][1000 genomes]
rs60632986	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6550756	0.87[GIH][hapmap];0.84[MKK][hapmap]
rs6769173	0.87[GIH][hapmap];0.84[MKK][hapmap]
rs6770091	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs6795968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6796840	0.87[GIH][hapmap]
rs6797907	0.89[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6798153	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs6800930	0.80[YRI][hapmap]
rs6805889	0.88[CEU][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs704534	0.85[JPT][hapmap]
rs716456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7374592	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7374774	0.89[ASN][1000 genomes]
rs7613091	0.89[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs7614667	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7630344	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs7631334	0.87[GIH][hapmap];0.84[MKK][hapmap]
rs778462	0.87[GIH][hapmap]
rs778482	0.83[EUR][1000 genomes]
rs778486	0.81[GIH][hapmap]
rs778506	0.83[GIH][hapmap];0.82[MKK][hapmap]
rs778508	0.83[GIH][hapmap]
rs778521	1.00[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs952134	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820922	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821419	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9830388	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs9830392	0.85[EUR][1000 genomes]
rs9836574	0.92[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs9839738	0.88[CEU][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9847958	0.83[YRI][hapmap]
rs9853489	0.83[YRI][hapmap]
rs9859651	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1004417	chr3:23318797-23389422	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4858069	STXBP5L	trans	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23367400-23391400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:23368000-23391000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:23380800-23389400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:23383000-23386000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:23384000-23389600	Weak transcription	GM12878-XiMat	blood
6	chr3:23384400-23391800	Weak transcription	Primary B cells from cord blood	blood
7	chr3:23384600-23385200	Enhancers	Psoas Muscle	Psoas
8	chr3:23384600-23390600	Weak transcription	Primary B cells from peripheral blood	blood

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