Variant report

Variant	rs2144478
Chromosome Location	chr6:146381445-146381446
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:146380713..146383200-chr6:146863558..146865271,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118508	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10223508	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10457792	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10457793	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10457794	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10457795	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1062067	0.80[ASN][1000 genomes]
rs10872582	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10872583	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11155452	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1133832	0.80[ASN][1000 genomes]
rs11755334	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12194437	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13198450	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13204280	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1331636	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1331637	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1331639	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1331643	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1331645	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1412081	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474871	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2073287	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2144477	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2207785	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2224120	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2224121	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247206	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2247211	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2247317	0.80[ASN][1000 genomes]
rs2250387	0.80[ASN][1000 genomes]
rs2254283	0.80[ASN][1000 genomes]
rs2254288	0.80[ASN][1000 genomes]
rs2256998	0.80[ASN][1000 genomes]
rs2265471	0.80[ASN][1000 genomes]
rs2265477	0.80[ASN][1000 genomes]
rs2265917	0.80[ASN][1000 genomes]
rs2265918	0.80[ASN][1000 genomes]
rs2265919	0.80[ASN][1000 genomes]
rs2328712	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2474356	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2492855	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2748482	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2748483	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2748484	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2748485	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2748486	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2748487	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2748499	0.92[EUR][1000 genomes]
rs2748500	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2748502	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2777474	0.82[ASN][1000 genomes]
rs2777476	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2777477	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2777484	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2814866	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2814867	0.92[EUR][1000 genomes]
rs2814869	0.92[EUR][1000 genomes]
rs2814874	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814875	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814876	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814877	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2814880	0.80[ASN][1000 genomes]
rs2892453	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923579	0.82[EUR][1000 genomes]
rs3924498	0.83[EUR][1000 genomes]
rs3924499	0.83[EUR][1000 genomes]
rs3924502	0.82[EUR][1000 genomes]
rs4075694	0.85[EUR][1000 genomes]
rs4075695	0.85[ASN][1000 genomes]
rs4075696	0.85[ASN][1000 genomes]
rs4243478	0.84[ASN][1000 genomes]
rs4280983	0.86[EUR][1000 genomes]
rs4314514	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4316025	0.81[ASN][1000 genomes]
rs4360151	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4391282	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4435956	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4566902	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4896852	0.86[EUR][1000 genomes]
rs56181683	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6570736	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570738	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6908063	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6910790	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6913797	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6914813	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6917482	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6922507	0.85[EUR][1000 genomes]
rs6923545	0.84[EUR][1000 genomes]
rs6924159	0.85[EUR][1000 genomes]
rs6926076	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6926657	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6930975	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6934467	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6938972	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7739418	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747576	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7753092	0.84[EUR][1000 genomes]
rs7753696	0.86[EUR][1000 genomes]
rs7755440	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs854145	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs864390	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs866473	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9322043	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9322046	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9322047	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9322048	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs932522	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9373485	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9376970	0.84[EUR][1000 genomes]
rs9376971	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9376975	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9386141	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9390365	0.83[EUR][1000 genomes]
rs9390377	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9399569	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9399571	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9399573	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9403755	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9403756	0.85[EUR][1000 genomes]
rs9403757	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403764	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9403765	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9403767	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9403768	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9497424	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9497425	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9497427	0.84[EUR][1000 genomes]
rs9497431	0.83[EUR][1000 genomes]
rs9497434	0.85[EUR][1000 genomes]
rs9497435	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs969694	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9791313	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	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
2	nsv1029440	chr6:146349442-146407453	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2144478	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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