Variant report

Variant	rs858964
Chromosome Location	chr6:27142614-27142615
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27140704..27142960-chr6:27805075..27807684,3	K562	blood:
2	chr6:27140776..27143304-chr6:27356728..27358330,2	K562	blood:
3	chr6:27130865..27132489-chr6:27141029..27143301,2	MCF-7	breast:
4	chr6:27141325..27142925-chr6:27790869..27793347,2	K562	blood:

Variant related genes	Relation type
ENSG00000184348	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000197238	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1028308	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10456352	0.80[JPT][hapmap]
rs11756275	0.85[JPT][hapmap]
rs12527111	0.85[JPT][hapmap]
rs2022272	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2142685	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs2393915	0.85[JPT][hapmap]
rs2393918	0.81[JPT][hapmap]
rs4582379	0.81[JPT][hapmap]
rs4713069	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6456767	0.81[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs6456768	0.85[JPT][hapmap]
rs6921388	0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs6925226	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6930508	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap]
rs7744759	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7747454	0.85[JPT][hapmap]
rs858976	0.80[JPT][hapmap]
rs9295730	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9379958	0.80[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs9379960	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393790	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393791	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9461335	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs994691	0.85[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs858964	ZNF389	cis	intralobular white matter	BrainEAC
rs858964	ZNF389	cis	brain	BrainEAC
rs858964	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27136800-27143800	Weak transcription	HSMMtube	muscle
2	chr6:27137400-27143800	Weak transcription	Hela-S3	cervix
3	chr6:27137400-27144000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:27137600-27144000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:27138200-27144000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:27141000-27144400	Weak transcription	Fetal Kidney	kidney
7	chr6:27142400-27143400	Flanking Active TSS	K562	blood

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