Variant report

Variant	rs10133874
Chromosome Location	chr14:79499339-79499340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10131645	0.81[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs10135754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10139452	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10139460	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10141828	0.89[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs10141996	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10142256	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10142652	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10143998	0.86[AMR][1000 genomes]
rs10146149	0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap]
rs10146180	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10146527	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10147558	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10147940	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10148388	0.83[EUR][1000 genomes]
rs10150011	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10151590	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11159391	1.00[CEU][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11159392	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11159395	0.89[CEU][hapmap]
rs11624311	0.81[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs11625343	0.89[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs11627661	0.87[CEU][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs11627905	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11627971	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11849134	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12147468	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs12147527	0.89[EUR][1000 genomes]
rs12147740	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs12323794	0.89[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12431671	0.81[CEU][hapmap]
rs12434809	0.88[CEU][hapmap]
rs12435865	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12436277	0.92[EUR][1000 genomes]
rs12586394	0.88[CEU][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12880287	0.94[EUR][1000 genomes]
rs12881434	0.85[CEU][hapmap]
rs12882464	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12887850	0.89[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs12894123	0.84[CEU][hapmap]
rs12895916	0.89[CEU][hapmap]
rs12897265	0.81[EUR][1000 genomes]
rs1405474	0.92[CEU][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes]
rs1532728	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1532729	0.92[EUR][1000 genomes]
rs154325	0.92[CEU][hapmap]
rs1547533	0.89[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1547535	0.85[AMR][1000 genomes]
rs1566675	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs17108558	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108575	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1875595	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1995411	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2035284	0.85[CEU][hapmap]
rs2062740	0.88[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2062741	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2062744	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2062746	0.89[CEU][hapmap]
rs2088966	0.88[CEU][hapmap];0.88[JPT][hapmap]
rs2088967	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs2202167	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[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]
rs2202168	0.94[ASW][hapmap];0.89[CEU][hapmap];0.89[GIH][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2202171	0.88[CEU][hapmap];0.88[JPT][hapmap]
rs2202175	0.81[CEU][hapmap];0.95[TSI][hapmap]
rs2202185	0.92[CEU][hapmap]
rs2221297	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2370895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370902	0.82[EUR][1000 genomes]
rs2620398	0.85[CEU][hapmap]
rs28706257	0.82[EUR][1000 genomes]
rs28831381	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2887887	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs31406	0.84[EUR][1000 genomes]
rs34121288	0.81[EUR][1000 genomes]
rs35916059	0.92[EUR][1000 genomes]
rs4517711	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4899732	0.84[CEU][hapmap]
rs4903811	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4903812	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4903813	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4903816	0.88[CEU][hapmap];0.86[AMR][1000 genomes]
rs4903819	0.88[CEU][hapmap]
rs4903820	0.89[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs4903823	0.89[CEU][hapmap]
rs4903825	0.82[EUR][1000 genomes]
rs4903830	0.88[CEU][hapmap]
rs4903833	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs61639937	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6574478	0.89[CEU][hapmap];0.86[AMR][1000 genomes]
rs6574480	0.88[CEU][hapmap]
rs6574492	0.89[CEU][hapmap];0.88[TSI][hapmap]
rs6574493	0.89[CEU][hapmap]
rs7142308	0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7142821	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7149325	0.83[CEU][hapmap]
rs7150552	0.81[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap]
rs7155818	0.88[CEU][hapmap]
rs7157779	0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7161610	0.85[CEU][hapmap]
rs72687406	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8004582	0.85[CEU][hapmap]
rs8005334	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs8006615	0.89[CEU][hapmap]
rs8006983	0.89[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8007813	0.89[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8008393	0.89[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8008781	0.88[EUR][1000 genomes]
rs8009329	0.91[EUR][1000 genomes]
rs8009383	0.85[CEU][hapmap];0.82[CHD][hapmap];0.86[TSI][hapmap]
rs8009417	1.00[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8010365	0.88[CEU][hapmap]
rs8010673	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs8011832	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8012099	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8014314	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8016232	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8016756	0.87[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8017018	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8017027	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8020811	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs872483	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs874316	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs874317	0.89[EUR][1000 genomes]
rs9323669	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9323670	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9323671	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs937648	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs9652299	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs997842	0.89[CEU][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917249	chr14:79388181-79574717	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1041991	chr14:79394408-79644886	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1037112	chr14:79412455-79527656	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv931412	chr14:79420297-79928269	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1046464	chr14:79478352-79514789	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	lncRNA	n/a	inside rSNPs	diseases
6	nsv1036542	chr14:79478352-79518230	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	lncRNA	n/a	inside rSNPs	diseases
7	nsv948724	chr14:79484233-79614043	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10133874	VASH1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:79495200-79506400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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