Variant report

Variant	rs9379968
Chromosome Location	chr6:27244590-27244591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27099008..27100568-chr6:27243071..27244881,2	K562	blood:
2	chr6:27218922..27222706-chr6:27243224..27246037,3	K562	blood:
3	chr6:27213988..27216649-chr6:27243557..27246224,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112812	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10946904	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2038044	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2295603	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2893911	0.89[CEU][hapmap]
rs3800314	0.86[ASN][1000 genomes]
rs3800319	0.89[CEU][hapmap]
rs4236043	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs4546474	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs4559087	0.92[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4713074	0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs5030956	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs6909479	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6910659	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6913724	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6914521	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7744605	0.80[AMR][1000 genomes]
rs7746841	0.88[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9366689	0.89[CEU][hapmap]
rs9368501	0.86[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs9468015	0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]

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	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
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9379968	HIST1H2BM	cis	cerebellum	SCAN
rs9379968	BTN3A2	cis	lymphoblastoid	seeQTL
rs9379968	HIST1H4B	cis	parietal	SCAN
rs9379968	BTN3A3	cis	cerebellum	SCAN
rs9379968	ZNF323	cis	parietal	SCAN
rs9379968	ZKSCAN3	cis	parietal	SCAN
rs9379968	ZNF184	cis	parietal	SCAN
rs9379968	BTN3A3	cis	parietal	SCAN
rs9379968	ZSCAN23	cis	parietal	SCAN
rs9379968	HMGN4	cis	lymphoblastoid	seeQTL
rs9379968	ZSCAN23	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27243000-27247400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:27243400-27244800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:27243600-27247400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:27243800-27247000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:27243800-27247200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:27243800-27247200	Weak transcription	A549	lung
7	chr6:27244200-27246800	Weak transcription	K562	blood

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