Variant report

Variant	rs11079824
Chromosome Location	chr17:46591320-46591321
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46585053..46590191-chr17:46590759..46593936,5	MCF-7	breast:
2	chr17:46583694..46585677-chr17:46589290..46592117,3	K562	blood:
3	chr17:46590407..46593001-chr17:46595445..46597263,2	MCF-7	breast:
4	chr17:46590857..46593060-chr17:46597939..46599663,2	K562	blood:
5	chr17:46578669..46581323-chr17:46590008..46592021,2	MCF-7	breast:
6	chr17:46589537..46591935-chr17:46661739..46663956,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10514953	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10853099	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10853100	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11079825	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11079826	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11079828	0.93[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11651168	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11652125	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11652746	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11867735	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11869101	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12450225	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12603662	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1509638	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1812501	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1987164	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2036764	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2325948	0.82[CEU][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2326013	0.92[EUR][1000 genomes]
rs2740760	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs4793564	0.83[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59961340	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60154639	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60859312	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62065845	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62065847	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62066684	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7214534	0.83[EUR][1000 genomes]
rs72829818	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72829824	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7501529	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8077407	0.94[AMR][1000 genomes]
rs925284	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9892607	0.84[EUR][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
rs11079824	HOXB2	Cis_1M	lymphoblastoid	RTeQTL
rs11079824	HOXB-AS1	cis	Whole Blood	GTEx
rs11079824	HOXB3	cis	Whole Blood	GTEx
rs11079824	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46585000-46591600	Weak transcription	HSMM	muscle
2	chr17:46587800-46591800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
3	chr17:46589200-46593600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr17:46590200-46592000	Enhancers	Placenta Amnion	Placenta Amnion
5	chr17:46590200-46592200	Flanking Active TSS	GM12878-XiMat	blood
6	chr17:46590400-46591400	Enhancers	Rectal Smooth Muscle	rectum
7	chr17:46590400-46591600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr17:46590400-46591600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:46590400-46591600	Bivalent Enhancer	Stomach Mucosa	stomach
10	chr17:46590400-46592200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:46590400-46592200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:46590400-46592200	Enhancers	A549	lung
13	chr17:46590600-46591400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:46590600-46591400	Enhancers	Colonic Mucosa	Colon
15	chr17:46590600-46591400	Enhancers	Gastric	stomach
16	chr17:46590600-46592000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:46590600-46592000	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr17:46590600-46592000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr17:46590800-46592000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr17:46590800-46599600	Weak transcription	Right Atrium	heart
21	chr17:46591000-46591400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr17:46591000-46591400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr17:46591000-46591400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr17:46591000-46591400	Enhancers	Colon Smooth Muscle	Colon
25	chr17:46591000-46591600	Enhancers	Primary hematopoietic stem cells	blood
26	chr17:46591000-46592000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr17:46591000-46592200	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr17:46591000-46592400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:46591200-46591400	Enhancers	H9 Cell Line	embryonic stem cell
30	chr17:46591200-46591400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:46591200-46591400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
32	chr17:46591200-46591400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr17:46591200-46591400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
34	chr17:46591200-46591400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr17:46591200-46591400	Bivalent Enhancer	Placenta	Placenta
36	chr17:46591200-46591800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr17:46591200-46591800	Bivalent Enhancer	Fetal Lung	lung
38	chr17:46591200-46592000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:46591200-46592000	Enhancers	K562	blood
40	chr17:46591200-46592200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr17:46591200-46599400	Weak transcription	Rectal Mucosa Donor 31	rectum

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