Variant report

Variant	rs6504281
Chromosome Location	chr17:46565412-46565413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46563248..46569374-chr17:46695616..46701359,7	K562	blood:
2	chr17:46564497..46566146-chr17:46575665..46577794,2	MCF-7	breast:
3	chr17:46564020..46565955-chr17:46568575..46570721,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11868098	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12939811	0.82[EUR][1000 genomes]
rs12946855	0.88[EUR][1000 genomes]
rs17703636	0.92[EUR][1000 genomes]
rs17703660	0.92[EUR][1000 genomes]
rs2202895	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34378400	0.88[EUR][1000 genomes]
rs35621842	0.84[EUR][1000 genomes]
rs4239210	0.84[ASN][1000 genomes]
rs4793854	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4793889	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55859232	0.81[EUR][1000 genomes]
rs56038617	0.81[EUR][1000 genomes]
rs62065846	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62066689	0.82[EUR][1000 genomes]
rs6504340	0.85[EUR][1000 genomes]
rs7207109	0.88[EUR][1000 genomes]
rs7207171	0.96[EUR][1000 genomes]
rs7222242	0.92[EUR][1000 genomes]
rs7225995	0.88[EUR][1000 genomes]
rs8064626	0.92[EUR][1000 genomes]
rs8066613	0.88[EUR][1000 genomes]
rs8071207	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8072250	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8073963	0.86[EUR][1000 genomes]
rs8074125	0.80[EUR][1000 genomes]
rs8079617	0.81[EUR][1000 genomes]
rs9904760	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9905940	0.85[EUR][1000 genomes]
rs9906950	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9989493	0.88[EUR][1000 genomes];0.84[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6504281	HOXB2	cis	Whole Blood	GTEx
rs6504281	HOXB-AS1	cis	Whole Blood	GTEx
rs6504281	HOXB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46555000-46566000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:46559200-46566200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:46560800-46566000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr17:46560800-46566400	Enhancers	HMEC	breast
5	chr17:46561200-46566000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr17:46561200-46566200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:46561200-46566200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr17:46561400-46566600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr17:46561400-46569400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr17:46561400-46569600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:46561800-46566000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:46561800-46567400	Weak transcription	Colon Smooth Muscle	Colon
13	chr17:46562000-46567600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr17:46562000-46569800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:46562400-46567800	Weak transcription	GM12878-XiMat	blood
16	chr17:46563600-46569200	Enhancers	K562	blood
17	chr17:46563800-46565600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr17:46564200-46567600	Weak transcription	Adipose Nuclei	Adipose
19	chr17:46564600-46565600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr17:46564600-46569400	Weak transcription	A549	lung
21	chr17:46564600-46569800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr17:46564600-46569800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr17:46564600-46569800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr17:46564800-46565800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr17:46564800-46566400	Enhancers	NHEK	skin
26	chr17:46564800-46567600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:46564800-46567600	Weak transcription	NHLF	lung
28	chr17:46564800-46569800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr17:46564800-46569800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:46564800-46569800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr17:46565000-46567600	Weak transcription	HSMMtube	muscle
32	chr17:46565000-46567800	Weak transcription	NH-A	brain
33	chr17:46565000-46569400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:46565000-46569800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:46565000-46569800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr17:46565000-46569800	Weak transcription	NHDF-Ad	bronchial
37	chr17:46565200-46565600	Weak transcription	HSMM	muscle
38	chr17:46565200-46566200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr17:46565400-46566400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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