Variant report

Variant	rs3809777
Chromosome Location	chr17:46695064-46695065
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46694465-46695265	H1-neurons	neurons:	n/a	n/a
2	SIN3AK20	chr17:46694911-46696287	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr17:46692107-46708447	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr17:46685805-46708856	PANC-1	pancreas:	n/a	n/a
5	SUZ12	chr17:46694967-46696374	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr17:46694951-46695827	K562	blood:	n/a	n/a
7	SUZ12	chr17:46688630-46700411	NT2-D1	testis:	n/a	n/a
8	POLR2A	chr17:46694805-46695238	H1-neurons	neurons:	n/a	n/a

No data

(count:12 , 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	chr17:46408330..46410117-chr17:46693519..46696056,2	K562	blood:
4	chr17:46694510..46697000-chr17:46702527..46704150,2	MCF-7	breast:
5	chr17:46408617..46416311-chr17:46693434..46699776,8	K562	blood:
6	chr17:46241394..46243371-chr17:46694152..46695794,2	K562	blood:
7	chr17:46390188..46393069-chr17:46694762..46697606,2	K562	blood:
8	chr17:46625273..46627562-chr17:46694776..46697171,2	K562	blood:
9	chr17:46463565..46466806-chr17:46694501..46697815,3	K562	blood:
10	chr17:46424070..46425698-chr17:46692561..46695178,2	K562	blood:
11	chr17:46384277..46387252-chr17:46693448..46695631,2	MCF-7	breast:
12	chr17:46453134..46455609-chr17:46694822..46696897,2	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
ENSG00000235300	Chromatin interaction
ENSG00000170689	Chromatin interaction
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11079831	0.87[ASN][1000 genomes]
rs16942777	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs16942817	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2303489	0.87[ASN][1000 genomes]
rs3096645	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs3096646	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs3744774	0.88[ASN][1000 genomes]
rs3809776	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3809778	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809781	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3826540	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3826541	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4619445	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7405887	0.97[ASN][1000 genomes]
rs881012	0.88[ASN][1000 genomes]
rs8844	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs890433	0.85[CEU][hapmap];0.87[ASN][1000 genomes]
rs890434	0.87[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:54 , 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	chr17:46689600-46695600	Weak transcription	K562	blood
4	chr17:46693000-46696600	Enhancers	A549	lung
5	chr17:46693600-46696200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr17:46694200-46695200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
7	chr17:46694600-46695400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr17:46694600-46695400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:46694600-46696000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
10	chr17:46694600-46696600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:46694600-46697000	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr17:46694800-46696200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
13	chr17:46694800-46696600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
14	chr17:46694800-46697000	Bivalent Enhancer	Fetal Stomach	stomach
15	chr17:46695000-46695200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr17:46695000-46695200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:46695000-46695200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr17:46695000-46695200	Bivalent Enhancer	Brain Hippocampus Middle	brain
19	chr17:46695000-46695200	Bivalent Enhancer	Fetal Intestine Small	intestine
20	chr17:46695000-46695200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
21	chr17:46695000-46695200	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
22	chr17:46695000-46695200	Bivalent/Poised TSS	Spleen	Spleen
23	chr17:46695000-46695200	Flanking Bivalent TSS/Enh	NHEK	skin
24	chr17:46695000-46695200	Bivalent/Poised TSS	NHLF	lung
25	chr17:46695000-46695400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr17:46695000-46695400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr17:46695000-46695400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:46695000-46695600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr17:46695000-46695600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:46695000-46695600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr17:46695000-46695600	Bivalent Enhancer	Right Ventricle	heart
32	chr17:46695000-46695600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
33	chr17:46695000-46695600	Flanking Bivalent TSS/Enh	HSMM	muscle
34	chr17:46695000-46695600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
35	chr17:46695000-46695800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
36	chr17:46695000-46695800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
37	chr17:46695000-46696000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:46695000-46696000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr17:46695000-46696000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
40	chr17:46695000-46696200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr17:46695000-46696200	Bivalent Enhancer	Fetal Intestine Large	intestine
42	chr17:46695000-46696200	Bivalent Enhancer	Placenta	Placenta
43	chr17:46695000-46696400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
44	chr17:46695000-46696400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
45	chr17:46695000-46696400	Bivalent Enhancer	Colon Smooth Muscle	Colon
46	chr17:46695000-46696600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr17:46695000-46696600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
48	chr17:46695000-46696600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
49	chr17:46695000-46696600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
50	chr17:46695000-46696600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood

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