Variant report

Variant	rs72829862
Chromosome Location	chr17:46658305-46658306
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CUX1	chr17:46658280-46658311	K562	blood:	n/a	n/a
2	UBTF	chr17:46657222-46658452	K562	blood:	n/a	n/a
3	SUZ12	chr17:46657913-46660550	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr17:46657828-46658409	K562	blood:	n/a	n/a
5	HEY1	chr17:46657878-46658423	K562	blood:	n/a	n/a
6	UBTF	chr17:46654046-46658362	K562	blood:	n/a	n/a
7	POLR2A	chr17:46657849-46658340	K562	blood:	n/a	n/a
8	SUZ12	chr17:46653107-46661081	NT2-D1	testis:	n/a	n/a
9	SPI1	chr17:46658219-46658512	GM12891	blood:	n/a	chr17:46658298-46658307
10	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
11	TCF7L2	chr17:46657383-46658749	HEK293	kidney:	n/a	chr17:46657965-46657981 chr17:46657966-46657980 chr17:46657967-46657977 chr17:46657968-46657977 chr17:46657965-46657981 chr17:46657969-46657978
12	POLR2A	chr17:46658091-46658338	HUVEC	blood vessel:	n/a	n/a
13	TEAD4	chr17:46657299-46658367	K562	blood:	n/a	n/a
14	CHD1	chr17:46655927-46662288	IMR90	lung:	n/a	chr17:46657663-46657673 chr17:46660648-46660658
15	TCF7L2	chr17:46657364-46658425	PANC-1	pancreas:	n/a	chr17:46657965-46657981 chr17:46657966-46657980 chr17:46657967-46657977 chr17:46657968-46657977 chr17:46657965-46657981 chr17:46657969-46657978
16	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46459433..46462163-chr17:46658202..46660838,2	K562	blood:
2	chr17:46525263..46527446-chr17:46657806..46659592,2	K562	blood:
3	chr17:46652243..46654179-chr17:46657727..46659805,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HOXB4-1	chr17:46656992-46659621	ENSG00000257178.1

Variant related genes	Relation type
HOXB4	TF binding region
MIR10A	TF binding region
HOXB3	TF binding region
ENSG00000200538	Chromatin interaction
ENSG00000120093	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs55682497	1.00[AFR][1000 genomes]
rs55786154	1.00[AFR][1000 genomes]
rs56314407	1.00[AFR][1000 genomes]
rs72827889	1.00[AFR][1000 genomes]
rs72829847	1.00[AFR][1000 genomes]
rs72829852	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72829860	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72829861	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72829863	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72829868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72829877	0.82[EUR][1000 genomes]
rs72829881	0.83[EUR][1000 genomes]
rs72829895	1.00[AFR][1000 genomes]
rs72831805	1.00[AFR][1000 genomes]
rs72831816	1.00[AFR][1000 genomes]
rs72831824	1.00[AFR][1000 genomes]
rs72831829	1.00[AFR][1000 genomes]
rs72831830	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS 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	335 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
10	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
11	nsv575480	chr17:46617019-46684929	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription 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	322 gene(s)	inside rSNPs	diseases
12	nsv908582	chr17:46617019-46698710	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	nsv457822	chr17:46620402-46698710	Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
17	nsv575481	chr17:46620402-46698710	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh 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	334 gene(s)	inside rSNPs	diseases
18	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
19	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
20	nsv457824	chr17:46625519-46693491	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised 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	332 gene(s)	inside rSNPs	diseases
21	nsv575483	chr17:46625519-46693491	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46653400-46660400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr17:46653600-46660200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr17:46653800-46658400	Active TSS	NHDF-Ad	bronchial
4	chr17:46656000-46659200	Flanking Active TSS	HUVEC	blood vessel
5	chr17:46656000-46660600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:46656000-46661200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr17:46656600-46658600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr17:46656600-46658600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
9	chr17:46656600-46658600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr17:46656600-46658800	Weak transcription	Aorta	Aorta
11	chr17:46656600-46659200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr17:46656800-46658400	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr17:46656800-46658600	Active TSS	Colonic Mucosa	Colon
14	chr17:46656800-46658800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
15	chr17:46656800-46658800	Weak transcription	Esophagus	oesophagus
16	chr17:46656800-46659000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
17	chr17:46656800-46659000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr17:46656800-46659000	Weak transcription	Spleen	Spleen
19	chr17:46657000-46658400	Active TSS	Fetal Kidney	kidney
20	chr17:46657000-46658800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr17:46657000-46658800	Active TSS	NHLF	lung
22	chr17:46657000-46659000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
23	chr17:46657000-46659000	Enhancers	GM12878-XiMat	blood
24	chr17:46657200-46658400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:46657200-46658400	Weak transcription	HSMMtube	muscle
26	chr17:46657400-46658800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
27	chr17:46657400-46658800	Flanking Active TSS	K562	blood
28	chr17:46657400-46659200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
29	chr17:46657600-46658800	Weak transcription	Right Atrium	heart
30	chr17:46657600-46659000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
31	chr17:46657800-46658400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
32	chr17:46657800-46659000	Flanking Active TSS	Rectal Smooth Muscle	rectum
33	chr17:46657800-46659600	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr17:46657800-46660200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr17:46658000-46658400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:46658000-46658400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr17:46658000-46658400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr17:46658000-46658800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr17:46658000-46658800	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr17:46658000-46658800	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr17:46658000-46659000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr17:46658000-46659000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr17:46658000-46659000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr17:46658000-46659800	Bivalent/Poised TSS	Lung	lung
45	chr17:46658000-46661000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr17:46658200-46658400	Bivalent Enhancer	Fetal Lung	lung
47	chr17:46658200-46658400	Bivalent Enhancer	Fetal Stomach	stomach
48	chr17:46658200-46658400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr17:46658200-46658400	Bivalent/Poised TSS	NH-A	brain
50	chr17:46658200-46658600	Weak transcription	Placenta Amnion	Placenta Amnion

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