Variant report

Variant	rs10513560
Chromosome Location	chr3:160710798-160710799
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10433352	0.81[CHD][hapmap]
rs10936216	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496196	0.81[JPT][hapmap]
rs12498008	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs12690576	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs13325518	0.89[CHD][hapmap];0.93[JPT][hapmap]
rs1374786	0.89[ASN][1000 genomes]
rs1374787	0.84[CEU][hapmap];0.83[CHD][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs1447608	1.00[CEU][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1447609	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530635	0.89[ASN][1000 genomes]
rs1530636	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562466	0.87[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs1580253	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1580254	0.84[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs1599382	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs16831758	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs16831796	0.81[CHD][hapmap]
rs1868104	0.81[JPT][hapmap]
rs1868108	0.84[CEU][hapmap]
rs1868109	0.83[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs1971240	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs2028988	0.81[JPT][hapmap]
rs2061580	0.82[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs2121721	1.00[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2376476	0.85[EUR][1000 genomes]
rs2376477	0.86[EUR][1000 genomes]
rs2889391	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34462546	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34884182	0.84[AMR][1000 genomes]
rs4608736	0.87[ASN][1000 genomes]
rs4679927	0.89[ASN][1000 genomes]
rs4679928	0.85[EUR][1000 genomes]
rs58189630	0.88[ASN][1000 genomes]
rs6441345	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441346	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763532	0.87[CHB][hapmap];0.93[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769927	0.85[AMR][1000 genomes]
rs6770180	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6787694	0.82[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs6791375	0.83[AMR][1000 genomes]
rs6797498	0.81[JPT][hapmap]
rs6798966	0.87[ASN][1000 genomes]
rs6808311	0.85[AMR][1000 genomes]
rs6808386	1.00[CEU][hapmap];0.80[JPT][hapmap];0.93[EUR][1000 genomes]
rs733948	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs7610732	0.81[JPT][hapmap]
rs7611005	0.84[EUR][1000 genomes]
rs7613316	1.00[CEU][hapmap];0.80[JPT][hapmap];0.93[EUR][1000 genomes]
rs7616249	1.00[CEU][hapmap];0.80[JPT][hapmap];0.95[EUR][1000 genomes]
rs7626904	0.86[EUR][1000 genomes]
rs7626985	0.87[EUR][1000 genomes]
rs7628389	0.85[CHD][hapmap]
rs7635796	1.00[CEU][hapmap];0.80[JPT][hapmap];0.93[EUR][1000 genomes]
rs7640874	1.00[CEU][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs7644586	1.00[CEU][hapmap];0.80[JPT][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs778644	0.89[ASN][1000 genomes]
rs778647	0.82[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs778650	0.89[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs778651	0.82[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs778652	0.80[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs778655	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs778656	0.89[ASN][1000 genomes]
rs778658	0.87[ASN][1000 genomes]
rs778661	0.86[ASN][1000 genomes]
rs778662	0.89[ASN][1000 genomes]
rs796610	0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs814092	0.89[ASN][1000 genomes]
rs898676	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs898677	0.83[CHD][hapmap]
rs898682	0.87[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs956447	0.84[CEU][hapmap]
rs9813700	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9818081	0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap]
rs9832109	0.83[CHD][hapmap]
rs9839984	0.81[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs9840600	0.92[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9846254	0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9857743	1.00[CEU][hapmap];0.80[JPT][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9858335	0.97[CHD][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs9860182	0.96[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9873705	0.85[AMR][1000 genomes]
rs9881807	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1007004	chr3:160695108-160718154	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10513560	C3orf57	cis	parietal	SCAN
rs10513560	PPM1L	cis	cerebellum	SCAN
rs10513560	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160705000-160720000	Weak transcription	Gastric	stomach
2	chr3:160706000-160711200	Weak transcription	Right Atrium	heart
3	chr3:160706400-160716000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:160708200-160712000	Weak transcription	Placenta	Placenta
5	chr3:160710200-160712400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:160710400-160710800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr3:160710600-160711600	Enhancers	Left Ventricle	heart

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