Variant report

Variant	rs3120662
Chromosome Location	chr1:152302865-152302866
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152297727..152299355-chr1:152302860..152305582,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10749669	0.93[CEU][hapmap];0.95[CHD][hapmap];0.91[MEX][hapmap]
rs10749670	0.93[CEU][hapmap];0.91[CHB][hapmap]
rs10788824	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs10888470	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs10888471	0.93[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs10888473	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs10888483	0.87[EUR][1000 genomes]
rs11204947	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs11204948	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap]
rs11204949	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs11204978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204980	0.93[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204981	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11583524	0.93[CEU][hapmap];0.86[CHB][hapmap]
rs11584340	0.93[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11584427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11586114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11586631	0.81[EUR][1000 genomes]
rs11587676	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs11588170	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11588174	0.93[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap]
rs12027807	0.80[ASN][1000 genomes]
rs12405241	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12405278	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12406105	0.82[EUR][1000 genomes]
rs12407156	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12407553	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12407748	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12407807	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1390488	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs1390490	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs1496045	0.93[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap]
rs1858479	0.82[ASN][1000 genomes]
rs1858480	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1858482	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2050631	0.94[ASN][1000 genomes]
rs2065955	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2065956	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2184950	0.85[AMR][1000 genomes]
rs2184953	0.86[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2338555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2338556	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3091276	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3120653	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3120659	0.93[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3120661	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3126055	0.82[AMR][1000 genomes]
rs3126056	0.83[AMR][1000 genomes]
rs3126058	0.84[AMR][1000 genomes]
rs3126060	0.86[AMR][1000 genomes]
rs3126062	0.86[AMR][1000 genomes]
rs3126066	0.93[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3126067	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3126072	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3126074	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3126079	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3126085	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3126088	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3126089	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3126090	0.87[ASW][hapmap];0.82[YRI][hapmap]
rs3126091	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3126092	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3126093	0.83[YRI][hapmap]
rs3126094	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3126095	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3126097	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3126098	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34188926	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41267154	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4369233	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4845423	0.93[CEU][hapmap];0.95[CHD][hapmap];0.91[MEX][hapmap]
rs4845736	1.00[CEU][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap]
rs4845745	0.93[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap]
rs4845750	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs55650366	0.80[EUR][1000 genomes]
rs55654502	0.82[EUR][1000 genomes]
rs57672167	0.90[AMR][1000 genomes]
rs58832908	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587666	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6661167	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6666382	0.93[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap]
rs6681433	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6681457	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6683653	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72697000	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72698906	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522925	0.85[EUR][1000 genomes]
rs7550106	0.93[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs877776	0.93[CEU][hapmap];0.95[CHD][hapmap]
rs9435974	0.85[AMR][1000 genomes]
rs9436062	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv998298	chr1:152288685-152319877	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3120662	GABPB2	cis	cerebellum	SCAN
rs3120662	S100A9	cis	parietal	SCAN
rs3120662	IVL	cis	parietal	SCAN
rs3120662	VPS45	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152286600-152322200	Weak transcription	Ovary	ovary
2	chr1:152300000-152303800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:152302000-152309600	Weak transcription	Aorta	Aorta

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