Variant report

Variant	rs9380028
Chromosome Location	chr6:27872759-27872760
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27870902..27873198-chr6:28100520..28102131,2	K562	blood:
2	chr6:27870989..27872855-chr6:27917496..27919210,2	K562	blood:
3	chr6:27871585..27873256-chr6:28048766..28051077,2	K562	blood:
4	chr6:27872438..27874402-chr6:28097309..28099187,2	MCF-7	breast:
5	chr6:27870682..27873346-chr6:28302621..28304824,2	MCF-7	breast:
6	chr6:27869790..27872813-chr6:27932103..27935630,3	K562	blood:

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000272009	Chromatin interaction
ENSG00000214374	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1015075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1321504	1.00[CEU][hapmap]
rs149943	0.95[CHD][hapmap];0.85[GIH][hapmap]
rs149990	0.95[CHD][hapmap];0.85[GIH][hapmap]
rs16893573	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16893601	1.00[CEU][hapmap]
rs175597	0.85[JPT][hapmap]
rs183225	0.85[JPT][hapmap]
rs188015	0.96[ASN][1000 genomes]
rs200466	0.85[JPT][hapmap]
rs200469	0.85[JPT][hapmap]
rs200473	0.85[JPT][hapmap]
rs200479	0.85[JPT][hapmap]
rs200482	0.85[JPT][hapmap]
rs200483	0.85[JPT][hapmap]
rs200484	0.85[JPT][hapmap]
rs200485	0.85[JPT][hapmap]
rs200490	0.85[JPT][hapmap]
rs200501	0.85[JPT][hapmap]
rs200948	0.85[JPT][hapmap]
rs200949	0.85[JPT][hapmap]
rs200953	0.85[JPT][hapmap]
rs200954	0.85[JPT][hapmap]
rs200965	0.85[JPT][hapmap]
rs200968	0.85[JPT][hapmap]
rs200973	0.85[JPT][hapmap]
rs200974	0.82[JPT][hapmap]
rs200975	0.85[JPT][hapmap]
rs200977	0.85[JPT][hapmap]
rs200981	0.85[JPT][hapmap]
rs200989	0.85[JPT][hapmap]
rs200990	0.85[JPT][hapmap]
rs200995	0.85[JPT][hapmap]
rs201002	0.85[JPT][hapmap]
rs202906	0.95[CHD][hapmap];0.85[GIH][hapmap]
rs2747054	0.85[JPT][hapmap]
rs370155	0.85[JPT][hapmap]
rs401763	0.85[JPT][hapmap]
rs4713122	0.82[JPT][hapmap]
rs666846	0.85[JPT][hapmap]
rs904142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9348779	0.85[JPT][hapmap]
rs9357052	0.82[JPT][hapmap]
rs9368535	0.85[JPT][hapmap]
rs9368536	0.85[JPT][hapmap]
rs9368537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380026	0.82[JPT][hapmap]
rs9380029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380031	1.00[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9380032	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9380041	0.83[AMR][1000 genomes]
rs9380045	1.00[CEU][hapmap]
rs9380051	0.95[CHD][hapmap]
rs9393882	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9468271	1.00[CEU][hapmap]
rs9468275	1.00[CEU][hapmap]

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	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
3	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
4	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases
5	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9380028	HIST1H4J	cis	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27871600-27874200	Weak transcription	Placenta	Placenta
2	chr6:27871600-27875600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:27871600-27875600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:27871600-27875600	Weak transcription	HMEC	breast
5	chr6:27871600-27875600	Weak transcription	NHEK	skin
6	chr6:27871600-27883200	Weak transcription	Hela-S3	cervix
7	chr6:27871800-27874000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:27871800-27875600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:27872200-27876200	Strong transcription	K562	blood

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