Variant report

Variant	rs380568
Chromosome Location	chr9:6055531-6055532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:6013951..6016263-chr9:6053852..6055883,2	MCF-7	breast:
2	chr9:6041127..6043265-chr9:6054435..6057249,2	MCF-7	breast:
3	chr9:6054654..6056123-chr9:6305613..6307254,7	MCF-7	breast:
4	chr9:5890360..5891992-chr9:6052880..6055803,2	K562	blood:
5	chr9:6055397..6056252-chr9:6305741..6306569,2	K562	blood:
6	chr9:5886117..5886694-chr9:6054993..6055882,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137040	Chromatin interaction
ENSG00000120215	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10124484	1.00[CHB][hapmap]
rs10739084	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10975412	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10975413	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10975416	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11506678	0.84[ASN][1000 genomes]
rs12337790	1.00[CHB][hapmap]
rs12339889	1.00[CHB][hapmap]
rs12341021	1.00[CHB][hapmap]
rs1330124	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1332292	0.85[EUR][1000 genomes]
rs1537285	0.85[EUR][1000 genomes]
rs1556470	0.85[EUR][1000 genomes]
rs1591044	0.85[EUR][1000 genomes]
rs168168	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1755531	0.85[EUR][1000 genomes]
rs189348	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1970089	0.85[EUR][1000 genomes]
rs1993912	1.00[CHB][hapmap]
rs2150969	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28706504	0.84[ASN][1000 genomes]
rs340887	0.85[EUR][1000 genomes]
rs340893	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs340894	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs340896	0.85[EUR][1000 genomes]
rs340901	0.87[EUR][1000 genomes]
rs340902	0.87[EUR][1000 genomes]
rs340903	0.87[EUR][1000 genomes]
rs340904	0.87[EUR][1000 genomes]
rs340905	0.87[EUR][1000 genomes]
rs340906	0.87[EUR][1000 genomes]
rs340918	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs340919	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs340921	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340922	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340923	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340924	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340925	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340926	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340933	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs340934	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs340935	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs343475	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343476	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343479	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs343489	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343490	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343491	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343495	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs343496	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs369996	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs371165	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs371454	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs372560	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs374672	0.85[EUR][1000 genomes]
rs375560	0.85[EUR][1000 genomes]
rs376690	0.85[EUR][1000 genomes]
rs378952	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs380888	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs390158	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs393556	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397505	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs397916	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs398561	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs399834	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs401731	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs401834	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs420445	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs425489	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs437389	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs441616	0.85[EUR][1000 genomes]
rs442851	0.85[EUR][1000 genomes]
rs443175	0.85[EUR][1000 genomes]
rs451974	0.85[EUR][1000 genomes]
rs454664	0.88[ASN][1000 genomes]
rs503384	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs503507	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs531759	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62558390	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs639247	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs694796	0.85[EUR][1000 genomes]
rs695013	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7859471	1.00[CHB][hapmap]
rs821164	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9407312	0.85[EUR][1000 genomes]
rs9408638	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs974936	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv613205	chr9:6032924-6332901	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv916394	chr9:6055497-6322471	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs380568	C9orf70	cis	parietal	SCAN
rs380568	JAK2	cis	cerebellum	SCAN
rs380568	SMARCA2	cis	parietal	SCAN
rs380568	C9orf68	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6053200-6055800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:6054800-6055800	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr9:6054800-6056000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:6054800-6056000	Enhancers	Hela-S3	cervix
5	chr9:6054800-6056000	Enhancers	HMEC	breast
6	chr9:6055000-6056000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr9:6055400-6055800	Enhancers	NHEK	skin

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