Variant report

Variant	rs2302582
Chromosome Location	chr4:8594683-8594684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8582157..8584012-chr4:8592733..8594974,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155269	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs3756181	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3775884	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775885	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796737	0.96[ASN][1000 genomes]
rs3796738	0.80[ASN][1000 genomes]
rs3796739	0.96[ASN][1000 genomes]
rs4696855	0.81[ASN][1000 genomes]
rs6820571	0.81[ASN][1000 genomes]
rs73213354	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213364	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7683057	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv878612	chr4:8534283-8618916	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1832730	chr4:8541086-9514568	Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
5	esv1843578	chr4:8541086-9514568	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
6	nsv878613	chr4:8554894-8618916	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv878614	chr4:8554894-8669619	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv878615	chr4:8566758-8625245	Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv878616	chr4:8566758-8669619	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv878617	chr4:8566758-9371116	ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	nsv1014219	chr4:8578779-8724531	Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv878618	chr4:8579758-8641696	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv878619	chr4:8579758-8669619	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv878620	chr4:8584879-8674871	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv470015	chr4:8584879-8729638	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv878621	chr4:8584879-9371116	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2302582	USP17	cis	lymphoblastoid	seeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8573400-8609400	Weak transcription	Right Atrium	heart
2	chr4:8593800-8595600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:8594000-8594800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
4	chr4:8594000-8595000	Bivalent Enhancer	Fetal Heart	heart
5	chr4:8594000-8595200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:8594000-8595200	Bivalent Enhancer	Fetal Lung	lung
7	chr4:8594000-8595400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr4:8594000-8595400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:8594000-8596200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr4:8594200-8594800	Bivalent/Poised TSS	Colonic Mucosa	Colon
11	chr4:8594200-8594800	Bivalent Enhancer	Fetal Brain Male	brain
12	chr4:8594200-8594800	Bivalent/Poised TSS	HepG2	liver
13	chr4:8594200-8595200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:8594200-8595200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
15	chr4:8594200-8595200	Active TSS	Hela-S3	cervix
16	chr4:8594200-8595400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:8594200-8595400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr4:8594200-8595400	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr4:8594200-8595400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr4:8594200-8595400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr4:8594200-8595600	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr4:8594200-8595600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:8594200-8595600	Active TSS	Ovary	ovary
24	chr4:8594200-8596000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
25	chr4:8594200-8596400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
26	chr4:8594400-8594800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:8594400-8594800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr4:8594400-8594800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:8594400-8594800	Active TSS	Placenta Amnion	Placenta Amnion
30	chr4:8594400-8594800	Bivalent/Poised TSS	Right Ventricle	heart
31	chr4:8594400-8594800	Flanking Bivalent TSS/Enh	NH-A	brain
32	chr4:8594400-8594800	Bivalent/Poised TSS	Osteobl	bone
33	chr4:8594400-8595000	Active TSS	H1 Cell Line	embryonic stem cell
34	chr4:8594400-8595000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:8594400-8595000	Bivalent/Poised TSS	HSMM	muscle
36	chr4:8594400-8595200	Bivalent Enhancer	A549	lung
37	chr4:8594400-8595400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:8594400-8595400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
39	chr4:8594400-8595400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:8594400-8595400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr4:8594400-8595600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:8594400-8595600	Active TSS	HSMMtube	muscle
43	chr4:8594400-8595600	Bivalent/Poised TSS	NHDF-Ad	bronchial
44	chr4:8594400-8595800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr4:8594400-8595800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:8594400-8596000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:8594600-8594800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
48	chr4:8594600-8594800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:8594600-8594800	Bivalent/Poised TSS	Adipose Nuclei	Adipose
50	chr4:8594600-8595000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links