Variant report

Variant	rs4793951
Chromosome Location	chr17:46678814-46678815
allele	C/T
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	EP300	chr17:46678679-46679514	A549	lung:	n/a	n/a
2	MAX	chr17:46678754-46683315	A549	lung:	n/a	chr17:46682913-46682922 chr17:46680035-46680045
3	BCL3	chr17:46678716-46679637	A549	lung:	n/a	n/a
4	SUZ12	chr17:46669440-46680361	NT2-D1	testis:	n/a	n/a
5	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
6	CTCF	chr17:46678619-46682966	A549	lung:	n/a	chr17:46680112-46680130 chr17:46682285-46682298 chr17:46681649-46681667 chr17:46680114-46680135
7	SIN3AK20	chr17:46678594-46680869	PANC-1	pancreas:	n/a	n/a
8	REST	chr17:46678659-46679729	A549	lung:	n/a	n/a
9	TCF7L2	chr17:46677342-46679150	HEK293	kidney:	n/a	chr17:46678723-46678739 chr17:46678723-46678739 chr17:46678727-46678736 chr17:46678724-46678738
10	TCF7L2	chr17:46677226-46679659	PANC-1	pancreas:	n/a	chr17:46678723-46678739 chr17:46678723-46678739 chr17:46678727-46678736 chr17:46678724-46678738
11	POLR2A	chr17:46678687-46678948	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a
13	TCF12	chr17:46678754-46683128	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46673414..46676816-chr17:46677264..46681067,4	MCF-7	breast:
2	chr17:46675371..46683952-chr17:46685648..46690575,16	MCF-7	breast:
3	chr17:46674931..46679280-chr17:46681348..46684289,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALCOCO2-8	chr17:46678790-46679025	ENSG00000233101.6
2	lnc-CALCOCO2-8	chr17:46678790-46679283	ENSG00000233101.6
3	lnc-CALCOCO2-8	chr17:46678790-46679254	ENSG00000233101.6
4	lnc-CALCOCO2-8	chr17:46678790-46679025	ENSG00000233101.6
5	lnc-CALCOCO2-8	chr17:46678790-46679025	NR_110331

Variant related genes	Relation type
HOXB6	TF binding region
HOXB-AS3	TF binding region
ENSG00000108511	Chromatin interaction
ENSG00000233101	Chromatin interaction
ENSG00000260027	Chromatin interaction
ENSG00000120093	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1062037	0.86[ASN][1000 genomes]
rs1123630	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12939324	0.83[EUR][1000 genomes]
rs12952262	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1529334	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28575348	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3087996	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35825473	0.86[ASN][1000 genomes]
rs4646993	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4793589	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4793938	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4793939	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4793943	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66459980	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67412921	0.86[ASN][1000 genomes]
rs872760	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9896015	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9909884	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9912500	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46672400-46682600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:46675600-46679200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr17:46675800-46679000	Weak transcription	Pancreas	Pancrea
4	chr17:46676000-46679200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:46676200-46679000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:46676200-46679800	Enhancers	K562	blood
7	chr17:46676400-46679000	Bivalent Enhancer	Fetal Intestine Large	intestine
8	chr17:46676400-46679000	Weak transcription	HSMMtube	muscle
9	chr17:46677000-46680000	Weak transcription	NHLF	lung
10	chr17:46677400-46684000	Active TSS	Fetal Kidney	kidney
11	chr17:46677800-46679200	Enhancers	Colon Smooth Muscle	Colon
12	chr17:46677800-46680600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr17:46678000-46679000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr17:46678000-46679200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr17:46678200-46679400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr17:46678200-46679800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr17:46678400-46679200	Flanking Active TSS	A549	lung
18	chr17:46678600-46679000	Flanking Active TSS	HSMM	muscle
19	chr17:46678600-46679000	Enhancers	HUVEC	blood vessel
20	chr17:46678600-46679200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:46678600-46679200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
22	chr17:46678600-46679200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr17:46678600-46680400	Active TSS	Colonic Mucosa	Colon
24	chr17:46678800-46679000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr17:46678800-46679000	Enhancers	Adipose Nuclei	Adipose
26	chr17:46678800-46679200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:46678800-46679200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
28	chr17:46678800-46679200	Active TSS	Rectal Smooth Muscle	rectum
29	chr17:46678800-46679400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr17:46678800-46679600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
31	chr17:46678800-46679600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr17:46678800-46679600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr17:46678800-46679600	Bivalent Enhancer	Fetal Stomach	stomach
34	chr17:46678800-46679600	Flanking Active TSS	NHDF-Ad	bronchial
35	chr17:46678800-46679800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
36	chr17:46678800-46679800	Flanking Active TSS	Hela-S3	cervix
37	chr17:46678800-46680000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
38	chr17:46678800-46680200	Bivalent Enhancer	Liver	Liver
39	chr17:46678800-46680200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr17:46678800-46680400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
41	chr17:46678800-46681600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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