Variant report

Variant	rs769189
Chromosome Location	chr6:28500235-28500236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr6:28500173-28500368	HepG2	liver:	n/a	chr6:28500235-28500249 chr6:28500236-28500252

No.	Distal block	Cell Line	Cell type
1	chr6:28490306..28492074-chr6:28498929..28501971,3	K562	blood:
2	chr6:28499295..28501079-chr6:28547721..28550016,2	K562	blood:
3	chr6:28499347..28503956-chr6:28505758..28508912,7	K562	blood:
4	chr6:28498885..28501651-chr6:28502273..28504670,3	K562	blood:
5	chr6:28490306..28492074-chr6:28498929..28501092,2	K562	blood:
6	chr6:28494181..28496072-chr6:28498095..28502015,3	K562	blood:
7	chr6:28455084..28458229-chr6:28499553..28502958,3	K562	blood:

Variant related genes	Relation type
GPX6	TF binding region
ENSG00000198704	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12660763	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12661782	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16894139	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs16894166	0.81[AMR][1000 genomes]
rs2064424	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071966	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2078035	0.87[EUR][1000 genomes]
rs2078439	0.84[EUR][1000 genomes]
rs2227228	0.83[CHD][hapmap]
rs2273106	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28382604	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2859355	0.83[CHD][hapmap]
rs2859356	0.85[CHD][hapmap]
rs35327256	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35921765	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs377514	0.87[EUR][1000 genomes]
rs380879	0.90[EUR][1000 genomes]
rs448450	0.90[EUR][1000 genomes]
rs4713166	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62402370	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62402378	0.84[AMR][1000 genomes]
rs6456824	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6921021	0.84[EUR][1000 genomes]
rs6933732	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6942252	0.81[AMR][1000 genomes]
rs72844230	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9468385	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs974334	0.83[CHD][hapmap]

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	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv601211	chr6:28483482-28521316	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs769189	BTN2A3	cis	cerebellum	SCAN
rs769189	HIST1H2BB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28500000-28502000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:28500000-28504400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr6:28500000-28504600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:28500200-28502200	Weak transcription	K562	blood

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