Variant report

Variant	rs62065845
Chromosome Location	chr17:46589990-46589991
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46578035..46580947-chr17:46589126..46591025,3	K562	blood:
2	chr17:46583694..46585677-chr17:46589290..46592117,3	K562	blood:
3	chr17:46575342..46577434-chr17:46588645..46590527,2	K562	blood:
4	chr17:46583450..46585256-chr17:46588689..46590687,2	MCF-7	breast:
5	chr17:46585053..46590191-chr17:46590759..46593936,5	MCF-7	breast:
6	chr17:46589537..46591935-chr17:46661739..46663956,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10514953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853099	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10853100	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11079824	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11079825	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11079826	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11651168	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11652125	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11652746	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11867735	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11869101	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12450225	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12603662	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1509638	0.87[AMR][1000 genomes]
rs1553754	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1812501	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987164	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2036764	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2325948	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4793564	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59961340	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60154639	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60859312	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62065847	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62066684	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214534	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72829818	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72829824	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7501529	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8077407	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs925284	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
3	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62065845	HOXB2	cis	Whole Blood	GTEx
rs62065845	HOXB-AS1	cis	Whole Blood	GTEx
rs62065845	HOXB3	cis	Whole Blood	GTEx
rs62065845	HOXB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46583600-46590200	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr17:46583800-46590400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:46583800-46590400	Weak transcription	Colon Smooth Muscle	Colon
4	chr17:46584000-46590200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:46584400-46590200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:46584400-46590400	Weak transcription	A549	lung
7	chr17:46585000-46590600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr17:46585000-46591600	Weak transcription	HSMM	muscle
9	chr17:46587800-46590400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr17:46587800-46591800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr17:46588400-46590400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr17:46589000-46590200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr17:46589200-46590200	Weak transcription	K562	blood
14	chr17:46589200-46590400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:46589200-46590400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr17:46589200-46590400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:46589200-46593600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:46589400-46590800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr17:46589600-46590200	Enhancers	GM12878-XiMat	blood

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