Variant report

Variant	rs3809775
Chromosome Location	chr17:46696416-46696417
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:26)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr17:46695969-46697602	PANC-1	pancreas:	n/a	chr17:46696732-46696742
2	CTBP2	chr17:46696014-46696697	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD1	chr17:46695766-46696589	IMR90	lung:	n/a	n/a
4	TBL1XR1	chr17:46695970-46696828	K562	blood:	n/a	n/a
5	CTCF	chr17:46695522-46696618	HCT-116	colon:	n/a	n/a
6	CCNT2	chr17:46696017-46696994	K562	blood:	n/a	n/a
7	FOSL2	chr17:46695838-46696449	A549	lung:	n/a	n/a
8	NR2F2	chr17:46695954-46697100	K562	blood:	n/a	n/a
9	RCOR1	chr17:46695937-46696716	K562	blood:	n/a	n/a
10	IRF1	chr17:46695943-46696715	K562	blood:	n/a	n/a
11	MAZ	chr17:46695945-46696745	K562	blood:	n/a	n/a
12	CREB1	chr17:46695947-46696836	K562	blood:	n/a	n/a
13	RAD21	chr17:46695857-46696428	MCF-7	breast:	n/a	n/a
14	CTCF	chr17:46696371-46696485	GM19240	blood:	n/a	n/a
15	UBTF	chr17:46695926-46696654	K562	blood:	n/a	n/a
16	RAD21	chr17:46695563-46696580	SK-N-SH	brain:	n/a	n/a
17	IRF1	chr17:46695936-46696592	K562	blood:	n/a	n/a
18	CTCF	chr17:46696400-46696550	GM12873	blood:	n/a	n/a
19	PML	chr17:46696010-46696495	K562	blood:	n/a	n/a
20	BACH1	chr17:46696129-46696520	K562	blood:	n/a	n/a
21	CTCF	chr17:46695724-46696430	HCT-116	colon:	n/a	n/a
22	POLR2A	chr17:46692107-46708447	PANC-1	pancreas:	n/a	n/a
23	CHD2	chr17:46695895-46696528	K562	blood:	n/a	n/a
24	POLR2A	chr17:46696317-46700591	K562	blood:	n/a	n/a
25	CTCF	chr17:46696391-46696464	GM19238	blood:	n/a	n/a
26	CTCF	chr17:46695873-46696449	MCF-7	breast:	n/a	n/a
27	POLR2A	chr17:46695067-46708834	K562	blood:	n/a	n/a
28	POLR2A	chr17:46685805-46708856	PANC-1	pancreas:	n/a	n/a
29	CTCF	chr17:46695667-46696692	A549	lung:	n/a	n/a
30	SMC3	chr17:46695349-46696548	SK-N-SH	brain:	n/a	n/a
31	CTCF	chr17:46696360-46696510	AG04450	lung:	n/a	n/a
32	POLR2A	chr17:46695508-46696787	K562	blood:	n/a	n/a
33	CTCF	chr17:46696392-46696465	Medullo	brain:	n/a	n/a
34	MAX	chr17:46696308-46696778	K562	blood:	n/a	n/a
35	E2F6	chr17:46696373-46696484	K562	blood:	n/a	n/a
36	RUNX3	chr17:46695912-46696585	GM12878	blood:	n/a	n/a
37	RUNX3	chr17:46695926-46696469	GM12878	blood:	n/a	n/a
38	CTCF	chr17:46695831-46696467	K562	blood:	n/a	n/a
39	ELF1	chr17:46695725-46696422	A549	lung:	n/a	n/a
40	CTCF	chr17:46696389-46696466	GM12878	blood:	n/a	n/a
41	JUND	chr17:46695959-46696714	K562	blood:	n/a	n/a
42	CBX3	chr17:46695923-46696824	K562	blood:	n/a	n/a
43	TEAD4	chr17:46695689-46696668	K562	blood:	n/a	n/a
44	CUX1	chr17:46696138-46696724	K562	blood:	n/a	n/a
45	RAD21	chr17:46695575-46696617	HCT-116	colon:	n/a	n/a
46	FOXM1	chr17:46695815-46696424	GM12878	blood:	n/a	n/a
47	GABPA	chr17:46696375-46696798	K562	blood:	n/a	chr17:46696633-46696647
48	RAD21	chr17:46695481-46696528	HCT-116	colon:	n/a	n/a
49	CTCF	chr17:46696392-46696431	GM12891	blood:	n/a	n/a
50	TEAD4	chr17:46695886-46696679	K562	blood:	n/a	n/a

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46694321..46697000-chr17:46864191..46866345,2	K562	blood:
2	chr17:46464628..46466806-chr17:46694501..46697277,2	K562	blood:
3	chr17:46102017..46103055-chr17:46695675..46696647,5	K562	blood:
4	chr17:46563248..46569374-chr17:46695616..46701359,7	K562	blood:
5	chr17:46384534..46385515-chr17:46695686..46696518,4	MCF-7	breast:
6	chr17:46212503..46213132-chr17:46695732..46696641,2	MCF-7	breast:
7	chr17:46681515..46685552-chr17:46695972..46700113,3	MCF-7	breast:
8	chr17:46333899..46335510-chr17:46695937..46698252,2	K562	blood:
9	chr17:46413747..46415915-chr17:46695597..46698773,3	K562	blood:
10	chr17:46581684..46585389-chr17:46696226..46700293,4	K562	blood:
11	chr17:46694510..46697000-chr17:46702527..46704150,2	MCF-7	breast:
12	chr17:46679660..46680612-chr17:46695724..46696977,8	K562	blood:
13	chr17:46633214..46633990-chr17:46696005..46696512,2	K562	blood:
14	chr17:46670925..46671654-chr17:46696367..46696928,2	K562	blood:
15	chr17:46102373..46103175-chr17:46695748..46696490,3	MCF-7	breast:
16	chr17:46408617..46416311-chr17:46693434..46699776,8	K562	blood:
17	chr17:46390188..46393069-chr17:46694762..46697606,2	K562	blood:
18	chr17:46429031..46429886-chr17:46695607..46696541,3	MCF-7	breast:
19	chr17:46625273..46627562-chr17:46694776..46697171,2	K562	blood:
20	chr17:46569833..46570442-chr17:46695977..46696577,2	K562	blood:
21	chr17:46463565..46466806-chr17:46694501..46697815,3	K562	blood:
22	chr17:46453134..46455609-chr17:46694822..46696897,2	K562	blood:
23	chr17:46413111..46413812-chr17:46695913..46696553,2	MCF-7	breast:
24	chr17:46679814..46680416-chr17:46695689..46696572,4	MCF-7	breast:
25	chr17:46534407..46535828-chr17:46695754..46696608,3	K562	blood:
26	chr17:46206531..46208867-chr17:46695496..46698467,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CALCOCO2-6	chr17:46694460-46696607	ENSG00000248304
2	lnc-HOXB9-1	chr17:46694457-46696602	NONHSAT054454

No data

Variant related genes	Relation type
HOXB8	TF binding region
ENSG00000233101	Chromatin interaction
ENSG00000108511	Chromatin interaction
ENSG00000170689	Chromatin interaction
ENSG00000120075	Chromatin interaction
ENSG00000235300	Chromatin interaction
ENSG00000120093	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1057201	0.83[ASN][1000 genomes]
rs11652932	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11652981	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12938558	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2303486	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2303487	0.94[ASN][1000 genomes]
rs2326016	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2875820	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3809780	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4793963	0.82[ASN][1000 genomes]
rs731748	0.82[ASN][1000 genomes]
rs890435	0.83[ASN][1000 genomes]
rs9913026	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46688600-46697000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr17:46689000-46698000	Bivalent/Poised TSS	Fetal Kidney	kidney
3	chr17:46693000-46696600	Enhancers	A549	lung
4	chr17:46694600-46696600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
5	chr17:46694600-46697000	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr17:46694800-46696600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
7	chr17:46694800-46697000	Bivalent Enhancer	Fetal Stomach	stomach
8	chr17:46695000-46696600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:46695000-46696600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
10	chr17:46695000-46696600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr17:46695000-46696600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
12	chr17:46695000-46696600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
13	chr17:46695000-46696600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
14	chr17:46695000-46696800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr17:46695000-46697000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
16	chr17:46695000-46697000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr17:46695200-46696800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr17:46695400-46696600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
19	chr17:46695600-46696600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
20	chr17:46695600-46696600	Bivalent Enhancer	GM12878-XiMat	blood
21	chr17:46695600-46697400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
22	chr17:46695800-46696600	Bivalent Enhancer	Colonic Mucosa	Colon
23	chr17:46695800-46697400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr17:46695800-46697400	Bivalent Enhancer	Fetal Lung	lung
25	chr17:46696000-46696600	Bivalent Enhancer	HMEC	breast
26	chr17:46696000-46696800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr17:46696000-46697000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr17:46696000-46697000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:46696000-46697000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:46696000-46697000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:46696000-46697000	Active TSS	K562	blood
32	chr17:46696200-46696600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr17:46696200-46696600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
34	chr17:46696200-46696600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:46696200-46696600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
36	chr17:46696200-46696600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
37	chr17:46696200-46696600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
38	chr17:46696200-46696600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr17:46696200-46696600	Bivalent Enhancer	Thymus	Thymus
40	chr17:46696200-46696600	Active TSS	NHDF-Ad	bronchial
41	chr17:46696200-46696600	Flanking Bivalent TSS/Enh	NHLF	lung
42	chr17:46696200-46696800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:46696200-46696800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
44	chr17:46696200-46696800	Bivalent/Poised TSS	HSMM	muscle
45	chr17:46696200-46696800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
46	chr17:46696200-46697000	Bivalent Enhancer	Fetal Thymus	thymus
47	chr17:46696200-46697400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
48	chr17:46696200-46698400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
49	chr17:46696400-46696600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr17:46696400-46696600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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