Variant report

Variant	rs890431
Chromosome Location	chr17:46686840-46686841
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	SUZ12	chr17:46686802-46688344	NT2-D1	testis:	n/a	n/a
2	TCF12	chr17:46686425-46687058	ECC-1	luminal epithelium:	n/a	chr17:46686993-46687000
3	POLR2A	chr17:46686211-46690442	SK-N-MC	brain:	n/a	n/a
4	TCF7L2	chr17:46686365-46687015	PANC-1	pancreas:	n/a	n/a
5	EP300	chr17:46686292-46686995	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr17:46685805-46708856	PANC-1	pancreas:	n/a	n/a
7	MAZ	chr17:46686443-46688186	K562	blood:	n/a	chr17:46687379-46687389 chr17:46687617-46687627 chr17:46687253-46687263
8	MAFF	chr17:46686536-46686865	K562	blood:	n/a	n/a
9	MAFK	chr17:46686517-46686978	K562	blood:	n/a	chr17:46686621-46686638
10	POLR2A	chr17:46686611-46688909	K562	blood:	n/a	n/a
11	UBTF	chr17:46686590-46686970	K562	blood:	n/a	n/a
12	POLR2A	chr17:46685788-46692102	PANC-1	pancreas:	n/a	n/a
13	SMARCB1	chr17:46686813-46689764	Hela-S3	cervix:	n/a	n/a
14	SUZ12	chr17:46686772-46688152	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46212650..46214229-chr17:46686261..46688122,2	MCF-7	breast:
2	chr17:46685746..46689281-chr17:46702801..46705653,3	MCF-7	breast:
3	chr17:46412297..46414059-chr17:46686711..46688269,2	MCF-7	breast:
4	chr17:46337445..46339514-chr17:46686634..46688158,2	MCF-7	breast:
5	chr17:46675371..46683952-chr17:46685648..46690575,16	MCF-7	breast:
6	chr17:46686493..46690300-chr17:46702976..46707350,6	MCF-7	breast:

Variant related genes	Relation type
HOXB3	TF binding region
HOXB6	TF binding region
HOXB7	TF binding region
ENSG00000233101	Chromatin interaction
ENSG00000170689	Chromatin interaction
ENSG00000242207	Chromatin interaction
ENSG00000108511	Chromatin interaction
ENSG00000120093	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10853101	0.84[JPT][hapmap]
rs2288276	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2288277	0.84[AMR][1000 genomes]
rs2288278	0.92[JPT][hapmap]
rs2288279	1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs2555109	0.80[ASN][1000 genomes]
rs2740752	1.00[JPT][hapmap]
rs3809782	0.84[JPT][hapmap]
rs4646992	0.81[AMR][1000 genomes]
rs6504397	0.89[ASW][hapmap]
rs6504411	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7405452	0.89[ASW][hapmap];0.83[CEU][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7406170	0.88[AMR][1000 genomes]
rs7406324	0.88[AMR][1000 genomes]
rs7406798	0.89[ASW][hapmap]
rs7406910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9221	0.83[CEU][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9903182	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9905793	0.83[AMR][1000 genomes]
rs9907987	0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[AMR][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	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
rs890431	CCDC56	cis	cerebellum	SCAN
rs890431	KAT2A	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46683600-46691000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr17:46686000-46687600	Flanking Active TSS	Colonic Mucosa	Colon
3	chr17:46686200-46687000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:46686200-46687000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr17:46686200-46687000	Enhancers	Adipose Nuclei	Adipose
6	chr17:46686200-46687200	Bivalent Enhancer	Fetal Stomach	stomach
7	chr17:46686200-46687200	Flanking Active TSS	Hela-S3	cervix
8	chr17:46686200-46687200	Flanking Active TSS	NHDF-Ad	bronchial
9	chr17:46686200-46687400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr17:46686200-46687400	Bivalent Enhancer	Placenta	Placenta
11	chr17:46686200-46687800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:46686200-46688200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr17:46686400-46687000	Flanking Active TSS	Fetal Kidney	kidney
14	chr17:46686400-46687000	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr17:46686400-46687200	Enhancers	GM12878-XiMat	blood
16	chr17:46686400-46687400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:46686400-46687400	Flanking Active TSS	A549	lung
18	chr17:46686400-46687600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr17:46686600-46687000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr17:46686600-46687000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr17:46686600-46687200	Flanking Active TSS	NHLF	lung
22	chr17:46686600-46687400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
23	chr17:46686600-46687600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:46686600-46687600	Flanking Active TSS	K562	blood
25	chr17:46686800-46687000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr17:46686800-46687000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
27	chr17:46686800-46687000	Enhancers	Rectal Smooth Muscle	rectum
28	chr17:46686800-46687000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
29	chr17:46686800-46687000	Active TSS	HSMM	muscle
30	chr17:46686800-46687000	Weak transcription	HSMMtube	muscle
31	chr17:46686800-46687200	Enhancers	Colon Smooth Muscle	Colon
32	chr17:46686800-46687200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr17:46686800-46687200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
34	chr17:46686800-46687400	Flanking Active TSS	HUVEC	blood vessel
35	chr17:46686800-46687600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:46686800-46687600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr17:46686800-46687600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion

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