Variant report

Variant	rs13204280
Chromosome Location	chr6:146415368-146415369
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10223507	0.96[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs10223508	0.81[EUR][1000 genomes]
rs10457792	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457793	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10457794	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10457795	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10872582	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10872583	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11155452	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11755334	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12194437	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13198450	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1331634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap]
rs1331636	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1331637	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1331639	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1331643	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1331645	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1412081	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474871	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2073287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2144477	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2144478	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2207785	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2224120	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2224121	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2247317	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2247666	0.96[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2265471	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2265472	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2265919	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2328712	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2474356	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2492855	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2748482	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2748483	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2748484	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2748485	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2748486	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2748487	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2748499	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2748500	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2748502	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2777476	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2777477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2777484	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2814863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs2814866	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2814867	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2814869	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2814874	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2814875	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2814876	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2814877	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2892453	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3924499	0.96[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs3924502	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs4075694	0.96[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs4075695	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4243478	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4280983	0.96[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs4314514	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4360151	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4391282	0.81[EUR][1000 genomes]
rs4896852	0.81[EUR][1000 genomes]
rs56181683	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6570736	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6570738	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6908063	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6913797	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914813	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6922507	0.96[CEU][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs6923545	0.96[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs6924159	0.80[EUR][1000 genomes]
rs6926076	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6926657	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6930975	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6934467	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6938972	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7739418	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7747576	0.81[EUR][1000 genomes]
rs7753092	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs7753696	0.96[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs7755440	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs854145	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs863820	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs864390	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs866473	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9322043	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9322046	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9322047	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9322048	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs932522	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9373485	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9376970	0.96[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs9376971	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9376975	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9386141	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs9390365	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs9390377	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9399571	0.81[EUR][1000 genomes]
rs9399573	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403755	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9403756	0.96[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs9403757	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9403764	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9403765	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403767	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9403768	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9497424	0.96[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs9497425	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9497427	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9497431	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs9497434	0.92[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs9497435	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs969694	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9791313	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv604839	chr6:146305810-146828922	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13204280	SHPRH	cis	parietal	SCAN
rs13204280	ULBP3	cis	parietal	SCAN
rs13204280	SHPRH	cis	cerebellum	SCAN
rs13204280	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146414200-146415400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr6:146414400-146415400	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr6:146414600-146415800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr6:146415000-146415400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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