Variant report

Variant	rs58554000
Chromosome Location	chr17:46095432-46095433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46064562..46065076-chr17:46095430..46096223,2	MCF-7	breast:
2	chr17:46058567..46060274-chr17:46094283..46095941,2	K562	blood:
3	chr17:46026392..46027250-chr17:46095165..46096377,5	K562	blood:
4	chr17:45919859..45920596-chr17:46095215..46095744,2	MCF-7	breast:
5	chr17:46055400..46056359-chr17:46095413..46096252,5	MCF-7	breast:
6	chr17:46094248..46097209-chr17:46632627..46635464,2	K562	blood:
7	chr17:46055365..46056387-chr17:46095357..46096410,11	K562	blood:
8	chr17:46046870..46049794-chr17:46095106..46097466,2	K562	blood:
9	chr17:46058567..46062223-chr17:46094441..46097254,3	K562	blood:
10	chr17:45920026..45921157-chr17:46095429..46096394,5	K562	blood:
11	chr17:46025314..46027169-chr17:46093324..46095871,2	K562	blood:
12	chr17:45918282..45919202-chr17:46095408..46096409,4	K562	blood:
13	chr17:45918292..45919402-chr17:46095322..46096165,4	MCF-7	breast:
14	chr17:46094604..46097136-chr17:46099608..46102510,2	K562	blood:
15	chr17:46055398..46056456-chr17:46095375..46096654,12	MCF-7	breast:
16	chr17:46027110..46029262-chr17:46094448..46097370,2	MCF-7	breast:
17	chr17:46089884..46092487-chr17:46093385..46095958,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000120093	Chromatin interaction
ENSG00000239552	Chromatin interaction
ENSG00000264019	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000141295	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1010230	0.81[EUR][1000 genomes]
rs12051	0.93[ASN][1000 genomes]
rs12600980	0.88[EUR][1000 genomes]
rs12601350	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12602131	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12602670	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12946143	0.91[EUR][1000 genomes]
rs1473117	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16951519	0.95[EUR][1000 genomes]
rs2023885	0.97[EUR][1000 genomes]
rs2109983	0.81[EUR][1000 genomes]
rs2229369	0.97[EUR][1000 genomes]
rs2240119	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240120	0.97[EUR][1000 genomes]
rs2240121	0.91[EUR][1000 genomes]
rs2285860	0.83[EUR][1000 genomes]
rs2325783	0.97[EUR][1000 genomes]
rs3785737	0.85[EUR][1000 genomes]
rs3815472	0.81[EUR][1000 genomes]
rs4995899	0.95[EUR][1000 genomes]
rs55920502	0.95[EUR][1000 genomes]
rs55982711	0.83[EUR][1000 genomes]
rs7224461	0.81[EUR][1000 genomes]
rs72823519	0.83[EUR][1000 genomes]
rs72823528	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72823532	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72823533	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs741058	0.81[EUR][1000 genomes]
rs757353	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8066049	0.84[EUR][1000 genomes]
rs8071199	0.85[EUR][1000 genomes]
rs8079616	0.81[EUR][1000 genomes]
rs978263	0.88[EUR][1000 genomes]
rs9890691	0.85[EUR][1000 genomes]
rs9898218	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58554000	CBX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46090000-46095800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:46090200-46100400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr17:46090200-46100400	Weak transcription	Brain Substantia Nigra	brain
4	chr17:46090400-46100800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr17:46091400-46095800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:46092600-46100400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr17:46092600-46100800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr17:46092600-46100800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr17:46092800-46100200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr17:46092800-46100400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr17:46092800-46100600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr17:46092800-46100600	Weak transcription	Fetal Brain Female	brain
13	chr17:46093600-46095800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr17:46093800-46100600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr17:46094000-46095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr17:46094000-46095600	Weak transcription	Placenta	Placenta
17	chr17:46094000-46098600	Weak transcription	HSMMtube	muscle
18	chr17:46094000-46100400	Weak transcription	HSMM	muscle
19	chr17:46094000-46101600	Weak transcription	K562	blood
20	chr17:46094600-46095800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr17:46094600-46096000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr17:46094800-46095800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:46094800-46095800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr17:46095000-46095800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr17:46095000-46095800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr17:46095000-46095800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr17:46095000-46095800	Enhancers	Fetal Thymus	thymus
28	chr17:46095000-46095800	Enhancers	A549	lung
29	chr17:46095000-46095800	Flanking Active TSS	GM12878-XiMat	blood
30	chr17:46095200-46095800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:46095200-46095800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr17:46095400-46095800	Enhancers	Fetal Brain Male	brain

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