Variant report

Variant	rs2525709
Chromosome Location	chr7:120559538-120559539
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	chr7:120554091..120556706-chr7:120557513..120559992,2	K562	blood:
2	chr7:120558221..120561390-chr7:120571663..120574345,3	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10225453	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10238554	0.87[ASN][1000 genomes]
rs10252911	0.90[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10257297	0.84[ASN][1000 genomes]
rs10257475	0.83[ASN][1000 genomes]
rs10266755	0.81[ASW][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10272601	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10274689	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10279837	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10282072	0.87[ASN][1000 genomes]
rs10953922	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11982493	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12669167	0.80[ASN][1000 genomes]
rs1557857	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17142995	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs17143001	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs17143009	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs1859316	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1859318	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1859319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2040762	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2058501	0.81[LWK][hapmap]
rs2074577	0.93[ASW][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];0.84[LWK][hapmap];0.81[ASN][1000 genomes]
rs2097806	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2107276	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2244863	0.93[ASW][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2244865	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2248890	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2524949	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2524951	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2525705	0.90[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525708	0.89[ASN][1000 genomes]
rs2525710	0.85[CEU][hapmap]
rs2525712	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2525713	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2525719	0.81[ASN][1000 genomes]
rs2525730	0.80[ASN][1000 genomes]
rs2525737	0.81[ASN][1000 genomes]
rs2525743	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721330	0.85[CEU][hapmap]
rs2721332	0.81[CEU][hapmap]
rs2721339	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2721341	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2721343	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2721347	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2721354	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2721363	0.93[ASW][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2721364	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721365	0.81[ASN][1000 genomes]
rs2721367	0.81[ASN][1000 genomes]
rs2721372	0.81[ASN][1000 genomes]
rs3757556	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs3757557	0.83[CHD][hapmap]
rs3779386	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3823859	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3823861	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap]
rs4141309	0.83[CHD][hapmap]
rs41624	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs41629	0.81[ASW][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs41632	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs41690	0.93[ASW][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs55855220	0.80[ASN][1000 genomes]
rs61452531	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6466759	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6466760	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6466761	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.81[ASN][1000 genomes]
rs6466762	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6944789	0.81[LWK][hapmap]
rs6953454	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6958947	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6959328	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6964344	0.82[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs6964786	0.80[ASN][1000 genomes]
rs6971854	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs6979247	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs714259	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs732568	0.89[ASN][1000 genomes]
rs73427866	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73429803	0.83[ASN][1000 genomes]
rs745167	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776721	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7781985	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7805211	0.81[ASN][1000 genomes]
rs9649429	0.83[ASN][1000 genomes]
rs996903	0.93[ASW][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.80[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	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv437030	chr7:120550667-120562313	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv438002	chr7:120556620-120559538	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2525709	TSPAN12	cis	parietal	SCAN
rs2525709	TSPAN12	cis	Artery Tibial	GTEx
rs2525709	RNF133	cis	cerebellum	SCAN
rs2525709	RNF148	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120556000-120567200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:120556600-120561600	Weak transcription	Fetal Heart	heart
3	chr7:120559000-120559800	Enhancers	HSMMtube	muscle
4	chr7:120559200-120559800	Enhancers	Fetal Muscle Leg	muscle

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