Variant report

Variant	rs11625343
Chromosome Location	chr14:79582780-79582781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 134 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10131645	0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap]
rs10133874	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]
rs10135754	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10135769	0.89[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs10139452	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10139460	1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs10141828	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10141996	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10142256	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10142652	0.81[EUR][1000 genomes]
rs10143998	0.89[EUR][1000 genomes]
rs10146149	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs10146180	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs10146527	0.81[EUR][1000 genomes]
rs10146542	0.89[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs10147558	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10147940	0.96[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10148388	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10150011	0.92[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs10151372	1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10151590	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11159391	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs11159395	1.00[CEU][hapmap]
rs11624311	0.81[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap]
rs11627661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11627905	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11627971	0.81[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap]
rs12147468	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12147740	1.00[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs12323794	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12431671	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs12432817	0.89[EUR][1000 genomes]
rs12434809	1.00[CEU][hapmap]
rs12435865	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12586394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12881434	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs12887850	1.00[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs12894123	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs12895916	1.00[CEU][hapmap]
rs12897265	0.88[EUR][1000 genomes]
rs1405474	0.81[CEU][hapmap];0.88[JPT][hapmap]
rs1532728	0.89[CEU][hapmap]
rs154325	0.84[CEU][hapmap]
rs1547533	1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1547535	0.82[EUR][1000 genomes]
rs1566675	1.00[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17108558	0.85[EUR][1000 genomes]
rs17108575	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1875595	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1995411	1.00[CEU][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes]
rs2035284	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2062740	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2062741	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2062744	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2062746	1.00[CEU][hapmap]
rs2088966	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2088967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2202167	0.89[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2202168	1.00[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs2202171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2202172	0.92[EUR][1000 genomes]
rs2202175	0.92[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2202179	0.90[EUR][1000 genomes]
rs2202180	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2202183	0.90[EUR][1000 genomes]
rs2202184	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2202185	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs2221297	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2221298	0.89[CEU][hapmap]
rs2370895	0.96[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs2370900	0.92[EUR][1000 genomes]
rs2370901	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2370902	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370926	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2620398	0.96[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28706257	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28831381	0.92[EUR][1000 genomes]
rs2887887	0.89[CEU][hapmap]
rs34121288	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4517711	0.83[EUR][1000 genomes]
rs4899732	0.96[CEU][hapmap]
rs4903811	0.81[EUR][1000 genomes]
rs4903812	0.81[EUR][1000 genomes]
rs4903813	0.83[EUR][1000 genomes]
rs4903816	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4903819	1.00[CEU][hapmap]
rs4903820	1.00[CEU][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs4903823	1.00[CEU][hapmap]
rs4903825	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4903830	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4903833	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59502714	0.94[ASN][1000 genomes]
rs61639937	0.89[EUR][1000 genomes]
rs6574478	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6574480	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6574492	1.00[CEU][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs6574493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs7142308	0.85[CEU][hapmap];0.93[TSI][hapmap]
rs7149325	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7150552	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs7155818	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7157779	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7161610	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs72687406	0.89[EUR][1000 genomes]
rs72687493	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8004582	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs8005334	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8006615	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8006983	1.00[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs8007813	1.00[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs8008393	1.00[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs8009383	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap]
rs8009417	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs8010365	1.00[CEU][hapmap]
rs8010673	1.00[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs8011832	1.00[CEU][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8012099	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8013072	0.90[EUR][1000 genomes]
rs8014314	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8016232	0.89[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs8016756	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8017018	1.00[CEU][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs8018180	0.90[EUR][1000 genomes]
rs8019071	0.90[EUR][1000 genomes]
rs8020811	1.00[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs872483	0.92[CEU][hapmap]
rs9323670	1.00[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9323671	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs937648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs997842	1.00[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][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	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
2	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
3	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
4	esv2761846	chr14:79522198-79629157	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11625343	VASH1	cis	cerebellum	SCAN
rs11625343	C14orf148	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:79579200-79584200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:79580200-79584000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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