Variant report

Variant	rs58460883
Chromosome Location	chr5:1795739-1795740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1793350..1795860-chr5:1944846..1947402,2	MCF-7	breast:
2	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
3	chr5:1762386..1764429-chr5:1795462..1797247,2	K562	blood:
4	chr5:1794905..1795739-chr7:139705398..139706186,2	HCT-116	colon:
5	chr5:1787615..1789328-chr5:1793761..1797388,3	K562	blood:

Variant related genes	Relation type
ENSG00000249326	Chromatin interaction
ENSG00000249116	Chromatin interaction
ENSG00000113430	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1018120	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10447190	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10447191	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11948846	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11953620	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11959171	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12515616	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13170104	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13173081	0.81[ASN][1000 genomes]
rs13178976	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13186183	0.83[ASN][1000 genomes]
rs2270826	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776147	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776148	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776150	0.95[ASN][1000 genomes]
rs41411146	0.83[ASN][1000 genomes]
rs4975732	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4975735	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4975844	0.84[ASN][1000 genomes]
rs4975846	0.91[ASN][1000 genomes]
rs4975847	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975850	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4975854	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67272124	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	nsv1033147	chr5:1717303-1815821	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1020703	chr5:1724199-1814288	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv537608	chr5:1724199-1814288	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv1024133	chr5:1736691-1826510	Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	nsv537609	chr5:1736691-1826510	Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs58460883	MRPL36	Cis_1M	lymphoblastoid	RTeQTL
rs58460883	MRPL36	cis	Muscle Skeletal	GTEx
rs58460883	MRPL36	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1785200-1796000	Weak transcription	Thymus	Thymus
2	chr5:1786800-1796000	Weak transcription	Gastric	stomach
3	chr5:1789200-1796400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:1789200-1796400	Weak transcription	Esophagus	oesophagus
5	chr5:1790200-1796200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:1790400-1796400	Weak transcription	Brain Anterior Caudate	brain
7	chr5:1790400-1796800	Weak transcription	Brain Hippocampus Middle	brain
8	chr5:1790600-1796200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:1790600-1796400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:1790600-1796600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:1790600-1797000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:1790600-1797000	Weak transcription	Fetal Lung	lung
13	chr5:1790600-1797800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:1790800-1796000	Weak transcription	Brain Substantia Nigra	brain
15	chr5:1790800-1796200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:1790800-1796400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:1790800-1796600	Weak transcription	Adipose Nuclei	Adipose
18	chr5:1790800-1797000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:1791000-1796000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:1791000-1796200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:1791000-1796200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:1791000-1796400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:1791000-1796400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:1791000-1796600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:1791000-1796600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:1791000-1798800	Weak transcription	Fetal Brain Male	brain
27	chr5:1791000-1800200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:1791200-1795800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr5:1791200-1796200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:1791400-1796600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:1791600-1796600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr5:1792200-1795800	Weak transcription	Fetal Intestine Small	intestine
33	chr5:1792400-1797600	Weak transcription	Fetal Kidney	kidney
34	chr5:1792800-1796800	Weak transcription	Fetal Intestine Large	intestine
35	chr5:1793000-1796400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:1793000-1796800	Weak transcription	K562	blood
37	chr5:1793200-1796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:1793200-1798800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr5:1793400-1796400	Weak transcription	Dnd41	blood
40	chr5:1793400-1797000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr5:1793600-1795800	Enhancers	HSMMtube	muscle
42	chr5:1793600-1796000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:1793600-1796200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr5:1793600-1796400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:1793600-1796600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:1793600-1796600	Weak transcription	Left Ventricle	heart
47	chr5:1793800-1796200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:1793800-1796200	Weak transcription	Liver	Liver
49	chr5:1793800-1796200	Weak transcription	Placenta	Placenta
50	chr5:1793800-1796200	Weak transcription	Right Ventricle	heart

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