Variant report

Variant	rs1987164
Chromosome Location	chr17:46569052-46569053
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:46563248..46569374-chr17:46695616..46701359,7	K562	blood:
2	chr17:46568685..46570931-chr17:46575612..46578799,3	MCF-7	breast:
3	chr17:46568782..46571366-chr17:46604713..46607657,2	MCF-7	breast:
4	chr17:46568691..46570864-chr17:46669281..46671058,2	K562	blood:
5	chr17:46568059..46570366-chr17:46679514..46681666,2	K562	blood:
6	chr17:46532115..46533858-chr17:46568103..46570537,2	MCF-7	breast:
7	chr17:46553255..46555504-chr17:46567161..46569215,2	K562	blood:
8	chr17:46566753..46569471-chr17:46581683..46584279,2	MCF-7	breast:
9	chr17:46564020..46565955-chr17:46568575..46570721,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000233101	Chromatin interaction
ENSG00000108511	Chromatin interaction

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

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

rs_ID	r²[population]
rs10514953	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10853099	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10853100	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11079824	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11079825	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11079826	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11079828	0.82[EUR][1000 genomes]
rs11651168	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11652125	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11652746	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11867735	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11869101	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12450225	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12603662	0.86[AMR][1000 genomes]
rs1509638	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1812501	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2036764	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2325948	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2326013	0.87[EUR][1000 genomes]
rs4793564	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59961340	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60154639	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60859312	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62065845	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62065847	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62066684	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72829818	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72829824	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7501529	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8077407	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs925284	0.97[AMR][1000 genomes];0.86[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	esv1002528	chr17:46566180-46575960	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1987164	HOXB2	Cis_1M	lymphoblastoid	RTeQTL
rs1987164	HOXB3	cis	Whole Blood	GTEx
rs1987164	HOXB2	cis	Whole Blood	GTEx
rs1987164	HOXB-AS1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46561400-46569400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr17:46561400-46569600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:46562000-46569800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:46563600-46569200	Enhancers	K562	blood
5	chr17:46564600-46569400	Weak transcription	A549	lung
6	chr17:46564600-46569800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:46564600-46569800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr17:46564600-46569800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:46564800-46569800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:46564800-46569800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:46564800-46569800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:46565000-46569400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:46565000-46569800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:46565000-46569800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr17:46565000-46569800	Weak transcription	NHDF-Ad	bronchial
16	chr17:46565600-46569800	Enhancers	Primary hematopoietic stem cells	blood
17	chr17:46566200-46569800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:46566400-46569200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr17:46566400-46569800	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr17:46566400-46569800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr17:46566400-46569800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr17:46566400-46569800	Weak transcription	Gastric	stomach
23	chr17:46566400-46569800	Weak transcription	HMEC	breast
24	chr17:46566600-46569400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr17:46566600-46569400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:46567800-46569200	Enhancers	GM12878-XiMat	blood
27	chr17:46567800-46569800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr17:46567800-46569800	Enhancers	Placenta	Placenta
29	chr17:46568000-46569600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:46568000-46569600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr17:46568000-46569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr17:46568200-46569200	Weak transcription	Fetal Kidney	kidney
33	chr17:46568200-46569800	Weak transcription	NH-A	brain
34	chr17:46568400-46569800	Enhancers	Adipose Nuclei	Adipose
35	chr17:46568400-46569800	Weak transcription	Colon Smooth Muscle	Colon
36	chr17:46568400-46569800	Weak transcription	HSMMtube	muscle
37	chr17:46568600-46569600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr17:46568600-46569800	Weak transcription	NHEK	skin
39	chr17:46568800-46569200	Weak transcription	HSMM	muscle
40	chr17:46568800-46569200	Weak transcription	NHLF	lung
41	chr17:46568800-46569800	Weak transcription	Psoas Muscle	Psoas
42	chr17:46568800-46569800	Enhancers	HUVEC	blood vessel
43	chr17:46569000-46569400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
44	chr17:46569000-46569800	Enhancers	Primary B cells from cord blood	blood
45	chr17:46569000-46569800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
46	chr17:46569000-46569800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr17:46569000-46569800	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr17:46569000-46569800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr17:46569000-46569800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr17:46569000-46569800	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links