Variant report

Variant	rs6416440
Chromosome Location	chr15:45041424-45041425
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:45038897..45041596-chr15:45044777..45047241,2	K562	blood:

Variant related genes	Relation type
ENSG00000185880	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10163110	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10444818	0.86[ASN][1000 genomes]
rs1137516	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11634059	1.00[CEU][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11634063	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11639157	1.00[CEU][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12912870	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1630168	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1669833	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1690313	0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs16974543	1.00[CEU][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs1720723	1.00[CEU][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs1720724	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1869125	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1901530	0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs1901538	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993152	0.82[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs1993153	0.91[ASN][1000 genomes]
rs2084835	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2167595	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2468067	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2470908	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2470913	0.82[ASN][1000 genomes]
rs2960206	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3100140	1.00[CEU][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3100141	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3110677	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759878	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759881	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923989	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4923990	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4923991	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4923993	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62024991	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62025968	1.00[EUR][1000 genomes]
rs62025969	0.97[EUR][1000 genomes]
rs6416439	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493110	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493111	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493112	0.91[ASN][1000 genomes]
rs6493114	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493116	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493118	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493119	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493120	0.81[ASN][1000 genomes]
rs6493124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493125	1.00[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493126	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493127	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs6493128	1.00[EUR][1000 genomes]
rs7151	0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165535	0.82[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs7168090	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7172357	1.00[EUR][1000 genomes]
rs7172376	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7496437	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7496559	0.94[EUR][1000 genomes]
rs7497862	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8035787	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8036223	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8038532	0.97[EUR][1000 genomes]
rs935885	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs935888	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs935889	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6416440	TRIM69	cis	lymphoblastoid	seeQTL
rs6416440	METT5D1	trans	lymphoblastoid	seeQTL

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

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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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