Variant report

Variant	rs9646424
Chromosome Location	chr17:46705605-46705606
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46701823-46705617	K562	blood:	n/a	n/a
2	MYC	chr17:46705299-46705734	K562	blood:	n/a	n/a
3	POLR2A	chr17:46701890-46705619	K562	blood:	n/a	n/a
4	YY1	chr17:46705084-46705648	K562	blood:	n/a	n/a
5	POLR2A	chr17:46692107-46708447	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr17:46701690-46705809	K562	blood:	n/a	n/a
7	UBTF	chr17:46704759-46707390	K562	blood:	n/a	n/a
8	POLR2A	chr17:46695067-46708834	K562	blood:	n/a	n/a
9	POLR2A	chr17:46685805-46708856	PANC-1	pancreas:	n/a	n/a
10	BHLHE40	chr17:46705265-46705607	K562	blood:	n/a	n/a
11	MAZ	chr17:46702137-46705806	K562	blood:	n/a	chr17:46703964-46703973 chr17:46703065-46703075 chr17:46703749-46703759 chr17:46704706-46704715
12	EP300	chr17:46705297-46705605	K562	blood:	n/a	n/a
13	MAX	chr17:46705299-46705633	K562	blood:	n/a	n/a
14	MAX	chr17:46705079-46705725	K562	blood:	n/a	n/a
15	ZNF143	chr17:46705479-46705674	K562	blood:	n/a	n/a
16	MAX	chr17:46705317-46705612	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:46705577-46705627	AG10803	skin:	n/a
2	chr17:46705577-46705627	ovcar-3	ovarian:	n/a
3	chr17:46705577-46705627	Jurkat	blood:	n/a
4	chr17:46705577-46705627	HCT-116	colon:	n/a
5	chr17:46705577-46705627	NH-A	brain:	n/a
6	chr17:46705577-46705627	A549	lung:	n/a
7	chr17:46705577-46705627	SK-N-MC	brain:	n/a
8	chr17:46705577-46705627	HL-60	blood:	n/a
9	chr17:46705577-46705627	CMK	blood:	n/a
10	chr17:46705577-46705627	HEEpiC	esophagus:	n/a
11	chr17:46705577-46705627	IMR90	lung:	fetal
12	chr17:46705577-46705627	HCF	heart:	n/a
13	chr17:46705577-46705627	Caco-2	colon:	n/a
14	chr17:46705577-46705627	BE2_C	brain:	n/a
15	chr17:46705577-46705627	MCF-7	breast:	n/a
16	chr17:46705577-46705627	PrEC	prostate:	n/a
17	chr17:46705577-46705627	HRE	kidney:	n/a
18	chr17:46705577-46705627	SK-N-SH	brain:	n/a
19	chr17:46705577-46705627	RPTEC	kidney:	n/a
20	chr17:46705577-46705627	AG04449	skin:	fetal
21	chr17:46705577-46705627	AG09319	gingival:	n/a
22	chr17:46705577-46705627	T-47D	breast:	n/a
23	chr17:46705577-46705627	LNCaP	prostate:	n/a
24	chr17:46705577-46705627	NHDF-neo	bronchial:	n/a
25	chr17:46705577-46705627	HAEpiC	amniotic membrane:	n/a
26	chr17:46705577-46705627	NT2-D1	testis:	n/a
27	chr17:46705577-46705627	HUVEC	blood vessel:	n/a
28	chr17:46705577-46705627	HRCEpiC	kidney:	n/a
29	chr17:46705577-46705627	HCM	heart:	n/a
30	chr17:46705577-46705627	HRPEpiC	eye:	n/a
31	chr17:46705577-46705627	PFSK-1	brain:	n/a
32	chr17:46705577-46705627	GM06990	blood:	n/a
33	chr17:46705577-46705627	Hepatocyte	liver:	n/a
34	chr17:46705577-46705627	HEK293	kidney:	embryo
35	chr17:46705577-46705627	SK-N-SH_RA	brain:	n/a
36	chr17:46705577-46705627	HMEC	breast:	n/a
37	chr17:46705577-46705627	AG09309	skin:	n/a
38	chr17:46705577-46705627	AG04450	lung:	fetal
39	chr17:46705577-46705627	HNPCEpiC	eye:	n/a
40	chr17:46705577-46705627	MCF10A-Er-Src	breast:	n/a
41	chr17:46705577-46705627	HIPEpiC	eye:	n/a
42	chr17:46705577-46705627	K562	blood:	n/a
43	chr17:46705577-46705627	NHBE	bronchial:	n/a
44	chr17:46705577-46705627	GM12891	blood:	n/a
45	chr17:46705577-46705627	HCPEpiC	choroid plexus:	n/a
46	chr17:46705577-46705627	BJ	skin:	n/a
47	chr17:46705577-46705627	HepG2	liver:	n/a
48	chr17:46705577-46705627	SAEC	small airway:	n/a
49	chr17:46705577-46705627	H1-hESC	embryonic stem cell:	embryo
50	chr17:46705577-46705627	ProgFib	skin:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46701571..46706598-chr17:47072048..47076281,6	K562	blood:
2	chr17:46618868..46624573-chr17:46700689..46705978,10	K562	blood:
3	chr17:46705274..46707056-chr17:46708654..46710864,2	MCF-7	breast:
4	chr17:46685746..46689281-chr17:46702801..46705653,3	MCF-7	breast:
5	chr17:46686493..46690300-chr17:46702976..46707350,6	MCF-7	breast:

No data

Variant related genes	Relation type
HOXB-AS4	TF binding region
HOXB9	TF binding region
HOXB-AS4	CpG island
HOXB9	CpG island
ENSG00000230148	Chromatin interaction
ENSG00000159217	Chromatin interaction
ENSG00000210741	Chromatin interaction
ENSG00000173917	Chromatin interaction
ENSG00000250838	Chromatin interaction
ENSG00000260027	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2303488	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34582033	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35085494	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4239158	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58702553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62064567	0.80[EUR][1000 genomes]
rs62064570	0.84[EUR][1000 genomes]
rs62064609	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71377382	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8066740	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9646424	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46704600-46706400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr17:46704800-46706200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr17:46705000-46708400	Weak transcription	A549	lung
4	chr17:46705200-46705800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
5	chr17:46705600-46705800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
6	chr17:46705600-46706000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
7	chr17:46705600-46706400	Bivalent/Poised TSS	Colonic Mucosa	Colon
8	chr17:46705600-46706400	Active TSS	K562	blood

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