Variant report

Variant	rs578659
Chromosome Location	chr5:179309065-179309066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179308524..179311732-chr5:179312804..179315984,3	K562	blood:
2	chr5:179307319..179310872-chr5:179333429..179336113,3	MCF-7	breast:
3	chr5:179306460..179309457-chr5:179314767..179316995,2	MCF-7	breast:
4	chr5:179299709..179302436-chr5:179308085..179309910,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs156101	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs156104	0.85[AMR][1000 genomes]
rs1684973	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2431123	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2431124	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2434411	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs248218	0.83[EUR][1000 genomes]
rs248219	0.83[EUR][1000 genomes]
rs248222	0.84[AMR][1000 genomes]
rs248252	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs27410	0.82[EUR][1000 genomes]
rs27411	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs30381	0.81[ASN][1000 genomes]
rs30382	0.81[ASN][1000 genomes]
rs30385	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs32437	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32438	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3734003	0.81[EUR][1000 genomes]
rs532795	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs574997	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs860706	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs88183	0.83[EUR][1000 genomes]
rs9957	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
7	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
9	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
10	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
11	nsv883286	chr5:179290845-179313656	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs578659	SQSTM1	Cis_1M	lymphoblastoid	RTeQTL
rs578659	TBC1D9B	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179286200-179310600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179286600-179310600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr5:179286600-179310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:179286600-179311400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr5:179287200-179333600	Weak transcription	Right Atrium	heart
6	chr5:179287800-179310000	Weak transcription	Fetal Brain Male	brain
7	chr5:179288400-179310600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:179289000-179309200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:179289200-179309200	Strong transcription	Fetal Brain Female	brain
10	chr5:179289400-179309400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:179289600-179328000	Strong transcription	Adipose Nuclei	Adipose
12	chr5:179290400-179309600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:179293800-179309400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:179295000-179309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:179295200-179334000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr5:179296800-179309400	Weak transcription	HUVEC	blood vessel
17	chr5:179298600-179309400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:179299800-179309600	Weak transcription	K562	blood
19	chr5:179300200-179309400	Strong transcription	Fetal Stomach	stomach
20	chr5:179300400-179310200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:179300600-179309200	Weak transcription	GM12878-XiMat	blood
22	chr5:179302200-179310600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:179302400-179310800	Weak transcription	Psoas Muscle	Psoas
24	chr5:179302600-179309600	Weak transcription	NH-A	brain
25	chr5:179303800-179309800	Weak transcription	Primary B cells from cord blood	blood
26	chr5:179303800-179309800	Weak transcription	Fetal Kidney	kidney
27	chr5:179304600-179309800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr5:179304600-179310600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr5:179305200-179309400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:179305200-179309400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:179305200-179309800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:179305200-179310600	Weak transcription	HSMMtube	muscle
33	chr5:179305400-179309200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr5:179305400-179309200	Weak transcription	Fetal Lung	lung
35	chr5:179305400-179309400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:179305400-179309400	Weak transcription	NHEK	skin
37	chr5:179305600-179309400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:179305600-179309400	Weak transcription	Osteobl	bone
39	chr5:179305600-179309600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:179305800-179309400	Weak transcription	Small Intestine	intestine
41	chr5:179305800-179309400	Weak transcription	HepG2	liver
42	chr5:179305800-179309400	Weak transcription	NHDF-Ad	bronchial
43	chr5:179305800-179310600	Weak transcription	Hela-S3	cervix
44	chr5:179306000-179309800	Weak transcription	HSMM	muscle
45	chr5:179306400-179309200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr5:179306400-179309200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:179306400-179309400	Weak transcription	HMEC	breast
48	chr5:179306600-179309400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:179306600-179309600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr5:179306800-179309200	Weak transcription	H1 Cell Line	embryonic stem cell

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