Variant report

Variant	rs3087996
Chromosome Location	chr17:46669363-46669364
allele	A/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	MAZ	chr17:46669362-46676749	IMR90	lung:	n/a	chr17:46669880-46669890 chr17:46671209-46671222 chr17:46671209-46671222 chr17:46669884-46669894 chr17:46673053-46673063
2	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
3	SIN3AK20	chr17:46668635-46670170	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46621559..46624647-chr17:46668034..46670671,3	K562	blood:
2	chr17:46555079..46557571-chr17:46668928..46671035,2	K562	blood:

Variant related genes	Relation type
HOXB3	TF binding region
HOXB-AS3	TF binding region
ENSG00000206805	Chromatin interaction
ENSG00000173917	Chromatin interaction
ENSG00000230148	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1062037	0.83[ASN][1000 genomes]
rs1123630	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1529334	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28575348	0.81[EUR][1000 genomes]
rs35825473	0.83[ASN][1000 genomes]
rs4646993	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4793589	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793938	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4793939	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793943	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4793951	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66459980	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67412921	0.83[ASN][1000 genomes]
rs872760	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9896015	0.80[EUR][1000 genomes]
rs9909884	0.81[EUR][1000 genomes]
rs9912500	0.81[EUR][1000 genomes];0.90[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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46663200-46672000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:46663800-46669600	Weak transcription	Pancreas	Pancrea
3	chr17:46664000-46670000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr17:46665400-46670000	Weak transcription	HSMMtube	muscle
5	chr17:46665600-46672400	Active TSS	NHDF-Ad	bronchial
6	chr17:46666000-46669600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr17:46666400-46669400	Weak transcription	HSMM	muscle
8	chr17:46666400-46669600	Weak transcription	Adipose Nuclei	Adipose
9	chr17:46666400-46670600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:46666400-46678600	Weak transcription	Hela-S3	cervix
11	chr17:46666800-46671000	Weak transcription	HUVEC	blood vessel
12	chr17:46666800-46671600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
13	chr17:46667600-46669400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr17:46667800-46669400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr17:46668000-46669400	Enhancers	Primary hematopoietic stem cells	blood
16	chr17:46668000-46669800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:46668000-46670000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:46668000-46671200	Weak transcription	K562	blood
19	chr17:46668000-46671600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr17:46668200-46669600	Weak transcription	GM12878-XiMat	blood
21	chr17:46668200-46669800	Genic enhancers	Rectal Mucosa Donor 31	rectum
22	chr17:46668400-46669600	Weak transcription	HMEC	breast
23	chr17:46668400-46669800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:46668400-46670200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr17:46668600-46669600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
26	chr17:46668600-46669800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr17:46668800-46670800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
28	chr17:46668800-46671400	Bivalent/Poised TSS	Fetal Lung	lung
29	chr17:46669000-46671200	Weak transcription	A549	lung
30	chr17:46669000-46671400	Bivalent/Poised TSS	NH-A	brain
31	chr17:46669000-46672200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr17:46669200-46669400	Active TSS	Colonic Mucosa	Colon
33	chr17:46669200-46669400	Active TSS	Stomach Smooth Muscle	stomach
34	chr17:46669200-46670000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
35	chr17:46669200-46670400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr17:46669200-46670400	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr17:46669200-46671600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr17:46669200-46671600	Active TSS	Colon Smooth Muscle	Colon
39	chr17:46669200-46671600	Bivalent/Poised TSS	Fetal Stomach	stomach
40	chr17:46669200-46672000	Active TSS	Rectal Smooth Muscle	rectum
41	chr17:46669200-46672400	Active TSS	Fetal Kidney	kidney
42	chr17:46669200-46672400	Active TSS	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links