Variant report

Variant	rs4793870
Chromosome Location	chr17:46581184-46581185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46579782..46582446-chr17:46602782..46604521,2	MCF-7	breast:
2	chr17:46578669..46581323-chr17:46590008..46592021,2	MCF-7	breast:
3	chr17:46580131..46581682-chr20:55568889..55570521,2	MCF-7	breast:
4	chr17:46574112..46575706-chr17:46580959..46582706,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1022088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1042815	0.88[TSI][hapmap]
rs11868098	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2202895	0.80[AFR][1000 genomes]
rs35755011	0.90[EUR][1000 genomes]
rs4793854	1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs4793889	0.86[ASN][1000 genomes]
rs4794733	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62065846	0.86[ASN][1000 genomes]
rs8071207	0.88[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs8072250	1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[ASN][1000 genomes]
rs9904760	1.00[JPT][hapmap];0.82[LWK][hapmap];0.83[ASN][1000 genomes]
rs9906950	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9989493	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4793870	SP6	cis	parietal	SCAN
rs4793870	HOXB3	cis	Whole Blood	GTEx
rs4793870	HOXB2	cis	Whole Blood	GTEx
rs4793870	HOXB2	Cis_1M	lymphoblastoid	RTeQTL
rs4793870	PRAC	cis	parietal	SCAN
rs4793870	HOXB-AS1	cis	Whole Blood	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46574600-46588000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:46574800-46582800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr17:46574800-46582800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:46574800-46582800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr17:46576800-46582000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:46577200-46582000	Enhancers	Fetal Stomach	stomach
7	chr17:46578400-46582800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr17:46578600-46582600	Weak transcription	HSMM	muscle
9	chr17:46578600-46583000	Weak transcription	HSMMtube	muscle
10	chr17:46578800-46582600	Weak transcription	NH-A	brain
11	chr17:46578800-46583000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:46578800-46583200	Weak transcription	NHLF	lung
13	chr17:46579000-46581600	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr17:46579200-46581600	Weak transcription	A549	lung
15	chr17:46580200-46582200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr17:46580200-46584600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr17:46580400-46582000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr17:46580600-46581800	Bivalent Enhancer	Fetal Heart	heart
19	chr17:46580800-46582000	Enhancers	Rectal Smooth Muscle	rectum
20	chr17:46580800-46582400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:46580800-46584000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr17:46581000-46581200	Bivalent Enhancer	Fetal Lung	lung
23	chr17:46581000-46581400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr17:46581000-46581400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:46581000-46581600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr17:46581000-46581600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:46581000-46581800	Bivalent Enhancer	Fetal Intestine Large	intestine
28	chr17:46581000-46581800	Enhancers	Placenta	Placenta
29	chr17:46581000-46581800	Enhancers	K562	blood
30	chr17:46581000-46582000	Enhancers	Colon Smooth Muscle	Colon

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