Variant report

Variant	rs2303488
Chromosome Location	chr17:46710980-46710981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr17:46710947-46711048	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr17:46710723-46711397	H1-hESC	embryonic stem cell:	n/a	chr17:46711256-46711266
3	USF1	chr17:46710808-46711097	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:46710961-46711402	K562	blood:	n/a	n/a
5	MAX	chr17:46710728-46711215	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTBP2	chr17:46710420-46711534	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr17:46710950-46711044	H1-hESC	embryonic stem cell:	n/a	n/a
8	SUZ12	chr17:46710292-46711548	H1-hESC	embryonic stem cell:	n/a	n/a
9	E2F6	chr17:46710749-46711203	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr17:46708495-46711074	PANC-1	pancreas:	n/a	n/a
11	HMGN3	chr17:46710840-46711323	K562	blood:	n/a	n/a
12	MAX	chr17:46710737-46711195	H1-hESC	embryonic stem cell:	n/a	n/a
13	GABPA	chr17:46710728-46711132	H1-hESC	embryonic stem cell:	n/a	n/a
14	USF1	chr17:46710795-46711167	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HOXB7-1	chr17:46710869-46711132	XLOC_012505
2	lnc-HOXB7-1	chr17:46710876-46714135	ENSG00000260027.1

No data

Variant related genes	Relation type
HOXB7	TF binding region
MIR196A1	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs34582033	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35085494	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4239158	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58702553	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71377382	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8066740	0.84[EUR][1000 genomes]
rs9646424	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised 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	364 gene(s)	inside rSNPs	diseases
5	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
6	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription 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	349 gene(s)	inside rSNPs	diseases
7	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers 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	356 gene(s)	inside rSNPs	diseases
8	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS 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	348 gene(s)	inside rSNPs	diseases
9	nsv543380	chr17:46686151-46721371	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2303488	HOXB2	cis	Thyroid	GTEx
rs2303488	HOXB2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46708400-46712200	Bivalent/Poised TSS	Colonic Mucosa	Colon
2	chr17:46709600-46712200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
3	chr17:46709800-46711000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
4	chr17:46709800-46711600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr17:46709800-46712200	Weak transcription	A549	lung
6	chr17:46710000-46711200	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
7	chr17:46710000-46711400	Bivalent/Poised TSS	Small Intestine	intestine
8	chr17:46710400-46711000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
9	chr17:46710400-46711000	Enhancers	K562	blood
10	chr17:46710400-46711200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
11	chr17:46710400-46711200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr17:46710400-46711200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:46710600-46711000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:46710600-46711400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr17:46710600-46711600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
16	chr17:46710800-46711000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
17	chr17:46710800-46711000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
18	chr17:46710800-46711000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
19	chr17:46710800-46711000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:46710800-46711000	Bivalent Enhancer	Gastric	stomach
21	chr17:46710800-46711000	Bivalent Enhancer	Psoas Muscle	Psoas
22	chr17:46710800-46711000	Bivalent/Poised TSS	HUVEC	blood vessel
23	chr17:46710800-46711200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr17:46710800-46711200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr17:46710800-46711400	Bivalent Enhancer	Lung	lung
26	chr17:46710800-46711400	Enhancers	Pancreas	Pancrea
27	chr17:46710800-46711400	Bivalent/Poised TSS	HSMM	muscle
28	chr17:46710800-46711600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr17:46710800-46711600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
30	chr17:46710800-46711800	Active TSS	Rectal Mucosa Donor 29	rectum

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