Variant report

Variant	rs60859312
Chromosome Location	chr17:46599035-46599036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46573441..46575512-chr17:46598331..46600721,2	MCF-7	breast:
2	chr17:46577718..46579309-chr17:46598159..46599775,2	K562	blood:
3	chr17:46598326..46601321-chr17:46698384..46701343,2	K562	blood:
4	chr17:46590857..46593060-chr17:46597939..46599663,2	K562	blood:
5	chr17:46593476..46595143-chr17:46597692..46599844,2	MCF-7	breast:
6	chr17:46598332..46601241-chr20:55512594..55514937,2	MCF-7	breast:
7	chr17:46577717..46579696-chr17:46597150..46599532,2	MCF-7	breast:
8	chr17:46598294..46600467-chr17:46652650..46655029,2	MCF-7	breast:
9	chr17:46597156..46601458-chr17:46601809..46606314,7	MCF-7	breast:
10	chr17:46598935..46600877-chr17:46608428..46610318,2	MCF-7	breast:
11	chr17:46569196..46571892-chr17:46596978..46599661,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000120093	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10514953	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853099	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10853100	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11079824	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11079825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11651168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11652125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11652746	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11867735	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11869101	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12450225	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12603662	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1509638	0.90[AMR][1000 genomes]
rs1553754	0.86[ASN][1000 genomes]
rs1812501	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1987164	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2036764	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2325948	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2326013	0.82[EUR][1000 genomes]
rs4793564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59961340	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60154639	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62065845	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62065847	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62066684	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214534	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72829818	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72829824	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7501529	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077407	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs925284	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][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	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
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS 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	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs60859312	HOXB3	cis	Whole Blood	GTEx
rs60859312	HOXB2	cis	Whole Blood	GTEx
rs60859312	HOXB-AS1	cis	Whole Blood	GTEx
rs60859312	HOXB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46590800-46599600	Weak transcription	Right Atrium	heart
2	chr17:46591200-46599400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr17:46592000-46604000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:46592200-46599400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr17:46592400-46599400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:46593800-46599400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:46594200-46599400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr17:46595200-46599600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr17:46596800-46599200	Enhancers	K562	blood
10	chr17:46597400-46599400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr17:46597800-46601200	Enhancers	NHLF	lung
12	chr17:46598000-46600200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
13	chr17:46598200-46599200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr17:46598200-46599400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr17:46598400-46599200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr17:46598400-46599400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr17:46598400-46599400	Weak transcription	HSMM	muscle
18	chr17:46598400-46599400	Weak transcription	NHDF-Ad	bronchial
19	chr17:46598600-46599400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
20	chr17:46598800-46599200	Weak transcription	HSMMtube	muscle
21	chr17:46598800-46599800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
22	chr17:46598800-46601200	Enhancers	Fetal Kidney	kidney
23	chr17:46598800-46601800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:46599000-46599200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
25	chr17:46599000-46599800	Bivalent Enhancer	Fetal Lung	lung
26	chr17:46599000-46600000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:46599000-46600600	Flanking Active TSS	A549	lung
28	chr17:46599000-46601200	Enhancers	Fetal Stomach	stomach

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