Variant report

Variant	rs9885928
Chromosome Location	chr6:28650353-28650354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28642383..28644323-chr6:28648282..28651107,2	K562	blood:
2	chr6:28072038..28073860-chr6:28648173..28650609,2	K562	blood:
3	chr6:28649582..28652211-chr6:28693042..28694734,2	K562	blood:
4	chr6:28649222..28651616-chr6:28694274..28696265,2	MCF-7	breast:
5	chr6:28564953..28566880-chr6:28649469..28651175,2	MCF-7	breast:
6	chr6:28303799..28306722-chr6:28648744..28650916,2	K562	blood:
7	chr6:28582959..28585078-chr6:28649793..28652398,2	K562	blood:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12180700	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12211927	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1319075	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1337585	0.87[EUR][1000 genomes]
rs1810619	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2394149	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs370520	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs380914	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs414205	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4143771	0.87[EUR][1000 genomes]
rs420478	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4289643	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs436827	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs450630	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6456825	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6456831	0.86[EUR][1000 genomes]
rs6902736	0.86[EUR][1000 genomes]
rs6925714	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6926221	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6926470	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7381993	0.85[EUR][1000 genomes]
rs7382112	0.87[EUR][1000 genomes]
rs7382146	0.89[EUR][1000 genomes]
rs7383248	0.84[EUR][1000 genomes]
rs7752875	0.80[EUR][1000 genomes]
rs9295772	0.82[ASN][1000 genomes]
rs9295777	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9348810	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9368568	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9378185	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9380079	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9380083	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393920	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393921	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9501180	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[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	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
2	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9885928	ZNF187	cis	cerebellum	SCAN
rs9885928	ZSCAN23	cis	parietal	SCAN
rs9885928	ZNF323	cis	cerebellum	SCAN
rs9885928	ZNF323	cis	parietal	SCAN
rs9885928	ZSCAN23	cis	cerebellum	SCAN
rs9885928	ZKSCAN3	cis	cerebellum	SCAN
rs9885928	ZNF192	cis	cerebellum	SCAN
rs9885928	HIST1H2BL	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28642600-28653800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:28649600-28651000	Bivalent Enhancer	Dnd41	blood
3	chr6:28649800-28650600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:28649800-28651000	Flanking Active TSS	K562	blood
5	chr6:28650200-28650400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:28650200-28651400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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