Variant report

Variant	rs17693963
Chromosome Location	chr6:27710165-27710166
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27704147..27707950-chr6:27708663..27711353,6	K562	blood:

Variant related genes	Relation type
ENSG00000216915	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10484399	1.00[CEU][hapmap]
rs13193480	0.82[EUR][1000 genomes]
rs13193542	0.82[EUR][1000 genomes]
rs13194781	1.00[CEU][hapmap]
rs13199649	1.00[CEU][hapmap]
rs13199772	1.00[CEU][hapmap]
rs13199906	1.00[CEU][hapmap]
rs13202291	0.81[EUR][1000 genomes]
rs13202295	0.82[EUR][1000 genomes]
rs13209332	1.00[CEU][hapmap]
rs13210634	1.00[CEU][hapmap]
rs13212318	1.00[CEU][hapmap]
rs13212651	1.00[CEU][hapmap]
rs13215275	1.00[CEU][hapmap]
rs13217620	1.00[CEU][hapmap]
rs13218875	1.00[CEU][hapmap]
rs16868061	1.00[ASN][1000 genomes]
rs16868094	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16868154	1.00[ASN][1000 genomes]
rs175597	0.91[CEU][hapmap]
rs17695758	1.00[CEU][hapmap]
rs17750747	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17751184	1.00[CEU][hapmap]
rs17763089	1.00[CEU][hapmap]
rs200481	0.91[CEU][hapmap]
rs200482	0.91[CEU][hapmap]
rs200483	0.91[CEU][hapmap]
rs200484	0.91[CEU][hapmap]
rs200485	0.91[CEU][hapmap]
rs200490	0.91[CEU][hapmap]
rs200501	0.91[CEU][hapmap]
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]
rs34706883	1.00[CEU][hapmap]
rs35037868	0.82[EUR][1000 genomes]
rs35501037	0.82[EUR][1000 genomes]
rs370155	0.91[CEU][hapmap]
rs401763	0.91[CEU][hapmap]
rs425335	1.00[CEU][hapmap]
rs6927093	1.00[ASN][1000 genomes]
rs72847313	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

Variant related diseases (count:3)

Disease	PMID	Source
Schizophrenia or bipolar disorder	24280982	GWAS catalog
Schizophrenia	22688191	GWAS catalog
Schizophrenia, schizoaffective disorder or bipolar disorder	24166486	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17693963	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs17693963	BTN3A2	trans	lymphoblastoid	seeQTL
rs17693963	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs17693963	LOC100270746	cis	lymphoblastoid	seeQTL
rs17693963	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs17693963	HLA-H	cis	multi-tissue	Pritchard
rs17693963	BTN3A2	cis	multi-tissue	Pritchard
rs17693963	HLA-A	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27705600-27710400	Weak transcription	K562	blood
2	chr6:27707000-27714600	Weak transcription	GM12878-XiMat	blood

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