Variant report

Variant	rs12938558
Chromosome Location	chr17:46701954-46701955
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 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	SUZ12	chr17:46701724-46704029	NT2-D1	testis:	n/a	n/a
3	POLR2A	chr17:46701890-46705619	K562	blood:	n/a	n/a
4	UBTF	chr17:46701859-46704464	K562	blood:	n/a	n/a
5	POLR2A	chr17:46701711-46705055	HCT-116	colon:	n/a	n/a
6	POLR2A	chr17:46692107-46708447	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr17:46701690-46705809	K562	blood:	n/a	n/a
8	POLR2A	chr17:46695067-46708834	K562	blood:	n/a	n/a
9	TCF12	chr17:46701920-46704621	A549	lung:	n/a	n/a
10	POLR2A	chr17:46685805-46708856	PANC-1	pancreas:	n/a	n/a
11	UBTF	chr17:46701700-46704430	K562	blood:	n/a	n/a
12	SUZ12	chr17:46701854-46705033	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr17:46701810-46705548	K562	blood:	n/a	n/a
14	HEY1	chr17:46701850-46704035	K562	blood:	n/a	chr17:46703893-46703908
15	SIN3AK20	chr17:46701774-46704402	PANC-1	pancreas:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46605320..46607362-chr17:46701075..46703388,2	K562	blood:
2	chr17:46701571..46706598-chr17:47072048..47076281,6	K562	blood:
3	chr17:46618868..46624573-chr17:46700689..46705978,10	K562	blood:
4	chr17:46178405..46180431-chr17:46699662..46702513,2	K562	blood:
5	chr17:46321872..46325036-chr17:46699113..46702600,4	K562	blood:
6	chr1:205717410..205719501-chr17:46701728..46703623,2	K562	blood:
7	chr17:46130623..46133195-chr17:46701253..46702809,2	K562	blood:
8	chr17:46701313..46703636-chr17:46794092..46795763,2	K562	blood:
9	chr17:46383770..46386641-chr17:46700022..46702743,2	K562	blood:
10	chr17:46463272..46465978-chr17:46700470..46702463,2	K562	blood:
11	chr17:46700166..46702886-chr17:46980635..46983541,2	K562	blood:
12	chr17:46123925..46127532-chr17:46701622..46704234,4	K562	blood:

No data

Variant related genes	Relation type
HOXB-AS4	TF binding region
ENSG00000108468	Chromatin interaction
ENSG00000159217	Chromatin interaction
ENSG00000173917	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000069275	Chromatin interaction
ENSG00000235300	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000230148	Chromatin interaction
ENSG00000250838	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1057201	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11652932	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11652981	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2303486	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303487	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2326016	0.96[ASN][1000 genomes]
rs2875820	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3809775	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3809780	0.95[ASN][1000 genomes]
rs4793963	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs731748	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs890435	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9913020	0.82[EUR][1000 genomes]
rs9913026	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
4	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
5	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
6	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
7	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
8	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
9	nsv908583	chr17:46617019-46704536	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv457823	chr17:46620402-46704536	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh 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	342 gene(s)	inside rSNPs	diseases
13	nsv575482	chr17:46620402-46704536	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
14	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
rs12938558	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46698200-46703400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr17:46698400-46703000	Bivalent/Poised TSS	Fetal Kidney	kidney
3	chr17:46698800-46704200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr17:46700000-46702200	Transcr. at gene 5' and 3'	K562	blood
5	chr17:46700000-46702800	Weak transcription	Gastric	stomach
6	chr17:46700800-46704000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:46701000-46702400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
8	chr17:46701800-46702000	Bivalent Enhancer	Primary T cells from cord blood	blood
9	chr17:46701800-46702000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr17:46701800-46702000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
11	chr17:46701800-46702200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr17:46701800-46702200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr17:46701800-46702200	Flanking Active TSS	A549	lung
14	chr17:46701800-46702400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:46701800-46702400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr17:46701800-46702400	Bivalent/Poised TSS	Colonic Mucosa	Colon
17	chr17:46701800-46702400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
18	chr17:46701800-46703600	Bivalent/Poised TSS	Fetal Intestine Large	intestine
19	chr17:46701800-46704400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum

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