Variant report

Variant	rs1540472
Chromosome Location	chr4:173602275-173602276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10016145	0.88[JPT][hapmap]
rs10024969	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10025150	0.82[JPT][hapmap]
rs10025544	0.82[JPT][hapmap]
rs10031656	0.82[JPT][hapmap]
rs10034993	0.82[JPT][hapmap]
rs10520242	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10866363	0.80[JPT][hapmap]
rs11132954	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs11132955	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs11132959	0.82[CHB][hapmap];0.90[MEX][hapmap]
rs11132964	0.82[JPT][hapmap]
rs11132967	0.82[JPT][hapmap]
rs11132968	0.82[JPT][hapmap]
rs11132970	0.82[JPT][hapmap]
rs1158684	0.83[JPT][hapmap]
rs11932974	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs11942645	0.82[JPT][hapmap]
rs12498347	0.81[JPT][hapmap]
rs12499966	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12501554	0.82[JPT][hapmap]
rs12502034	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12502278	0.80[CEU][hapmap]
rs12502339	0.82[JPT][hapmap]
rs12505471	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12509227	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12510199	1.00[CEU][hapmap]
rs12510770	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12510844	0.83[EUR][1000 genomes]
rs12511707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12511715	0.90[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs12513314	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12643395	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12643742	0.82[JPT][hapmap]
rs12643816	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs12645440	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12646897	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12647340	0.84[JPT][hapmap]
rs12649426	0.84[JPT][hapmap]
rs12651320	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13144747	0.82[JPT][hapmap]
rs13146563	0.84[JPT][hapmap]
rs1347698	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1347700	0.84[JPT][hapmap]
rs1347702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs1347705	0.82[JPT][hapmap]
rs1437828	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1437840	0.90[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1437842	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs1455130	0.80[CEU][hapmap];0.85[GIH][hapmap]
rs1540466	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap]
rs1540468	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1540471	0.90[CEU][hapmap];0.90[CHB][hapmap]
rs1551664	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs1551665	0.80[CEU][hapmap]
rs17058683	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17058705	0.90[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap];0.83[EUR][1000 genomes]
rs17058736	0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17058752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17058802	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs17058876	0.82[JPT][hapmap]
rs17058882	0.89[CEU][hapmap]
rs17058886	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs17308944	0.84[JPT][hapmap]
rs180146	0.90[CEU][hapmap]
rs1898554	0.84[JPT][hapmap]
rs1946797	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2043781	0.89[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2043782	0.82[JPT][hapmap]
rs2118441	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36081927	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4522845	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4569731	0.81[CHB][hapmap];1.00[MEX][hapmap]
rs4608790	0.82[JPT][hapmap]
rs4695771	0.84[JPT][hapmap]
rs4695932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695991	0.83[EUR][1000 genomes]
rs4696014	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696032	0.80[CEU][hapmap]
rs58774009	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61077359	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62330792	0.83[EUR][1000 genomes]
rs62330815	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62330816	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62330818	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62330819	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62330820	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6553657	0.82[JPT][hapmap]
rs6812449	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6817631	0.82[JPT][hapmap]
rs6819460	0.82[JPT][hapmap]
rs6821734	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6827154	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6838201	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6842805	0.81[JPT][hapmap]
rs6844200	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs7376615	0.82[JPT][hapmap]
rs7378115	0.82[JPT][hapmap]
rs7435993	0.81[ASN][1000 genomes]
rs7438724	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs747493	0.90[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs748347	0.84[JPT][hapmap]
rs7659511	0.84[JPT][hapmap]
rs7664183	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7688630	0.82[JPT][hapmap]
rs7694886	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7699074	0.82[MEX][hapmap]
rs837196	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9312527	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs9992822	0.82[JPT][hapmap]
rs9997085	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031592	chr4:173112542-173662991	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537359	chr4:173112542-173662991	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534293	chr4:173121379-173606082	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv880685	chr4:173562564-173661711	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv880613	chr4:173569281-173661711	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3327952	chr4:173591786-173805861	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1540472	SAP30	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173601600-173606000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr4:173602000-173602400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:173602000-173602400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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