Variant report

Variant	rs13193480
Chromosome Location	chr6:27702561-27702562
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27669358..27671049-chr6:27700076..27702911,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10484399	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13192965	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13193542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13194781	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13195636	1.00[CEU][hapmap]
rs13195728	0.92[EUR][1000 genomes]
rs13199649	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13199772	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13199906	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13202291	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13202295	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13202775	0.87[EUR][1000 genomes]
rs13209332	1.00[CEU][hapmap]
rs13210634	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13212318	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13212651	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13215275	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13217620	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13218875	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs175597	0.91[CEU][hapmap]
rs17693963	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17695758	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17749927	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17750747	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17751184	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17763089	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs200481	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs200482	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs200483	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs200484	0.91[CEU][hapmap]
rs200485	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs200489	0.83[EUR][1000 genomes]
rs200490	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs200497	0.81[EUR][1000 genomes]
rs200501	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs200948	0.91[CEU][hapmap]
rs200949	0.91[CEU][hapmap]
rs200953	0.91[CEU][hapmap]
rs200954	0.91[CEU][hapmap]
rs200977	0.91[CEU][hapmap]
rs200981	0.89[CEU][hapmap]
rs200989	0.91[CEU][hapmap]
rs200990	0.91[CEU][hapmap]
rs200995	0.91[CEU][hapmap]
rs201002	0.91[CEU][hapmap]
rs2747054	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs34064842	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34105070	0.87[EUR][1000 genomes]
rs34194357	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34409918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34432857	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34706883	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs34718920	0.92[EUR][1000 genomes]
rs34788973	0.85[EUR][1000 genomes]
rs35037868	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35202262	1.00[AFR][1000 genomes]
rs35339855	1.00[AFR][1000 genomes]
rs35501037	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35715914	0.94[EUR][1000 genomes]
rs35819751	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs36116761	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs370155	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs390764	0.83[EUR][1000 genomes]
rs401754	0.83[EUR][1000 genomes]
rs401763	0.91[CEU][hapmap]
rs425335	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs45509595	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56405707	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61742093	0.85[EUR][1000 genomes]
rs66868086	0.89[EUR][1000 genomes]
rs67040724	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs67101035	0.92[EUR][1000 genomes]
rs67652222	0.92[EUR][1000 genomes]
rs71559038	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71559050	0.92[EUR][1000 genomes]
rs71559054	0.85[EUR][1000 genomes]
rs72845046	0.92[EUR][1000 genomes]
rs72845070	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72847313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9368531	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv970372	chr6:27695204-27708579	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv981370	chr6:27696520-27708579	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13193480	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs13193480	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs13193480	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27702200-27706000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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