Variant report

Variant	rs62338062
Chromosome Location	chr5:1824353-1824354
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:1819853..1822198-chr5:1823585..1825204,2	MCF-7	breast:
2	chr5:1823492..1825147-chr5:1825325..1826849,2	MCF-7	breast:
3	chr5:1801086..1802656-chr5:1824054..1826100,2	MCF-7	breast:
4	chr5:1823993..1826824-chr5:1830176..1831799,2	K562	blood:
5	chr5:1824315..1827809-chr5:1864869..1867236,3	MCF-7	breast:
6	chr5:1823993..1826108-chr5:1830299..1832827,2	K562	blood:
7	chr5:1820025..1823818-chr5:1823864..1826357,3	K562	blood:
8	chr5:1823728..1826019-chr5:1881609..1883896,2	MCF-7	breast:
9	chr5:1818595..1823818-chr5:1824144..1826436,4	K562	blood:
10	chr5:1813864..1817727-chr5:1823867..1827166,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000113430	Chromatin interaction
ENSG00000171421	Chromatin interaction
ENSG00000145494	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10074291	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10475109	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10866526	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11739312	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11740602	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11740753	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11741881	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11748427	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750565	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1546252	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1546253	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17535295	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17535721	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2131588	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2131589	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172530	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2353585	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3752844	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3756344	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3776152	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3776154	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4147775	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4275010	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4277951	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4296838	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4296839	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4304110	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4416633	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4588629	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60542979	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62338060	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62338061	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6859338	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6862914	0.89[ASN][1000 genomes]
rs6864281	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6868515	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6873986	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6880885	0.89[ASN][1000 genomes]
rs6881253	0.89[ASN][1000 genomes]
rs6890404	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6894566	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7701970	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7703762	0.89[ASN][1000 genomes]
rs7714300	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
6	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
7	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
8	nsv461911	chr5:1820557-1855301	Strong transcription Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv596890	chr5:1820557-1855301	Enhancers Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	nsv596891	chr5:1822326-1880891	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv880647	chr5:1822326-1880891	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv881619	chr5:1822326-1886471	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv881557	chr5:1822326-1932463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62338062	MRPL36	cis	Muscle Skeletal	GTEx
rs62338062	MRPL36	Cis_1M	lymphoblastoid	RTeQTL
rs62338062	MRPL36	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1802200-1827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:1802800-1825000	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:1802800-1825800	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:1802800-1826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr5:1802800-1828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:1803000-1825000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr5:1803000-1825000	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr5:1803000-1825600	Strong transcription	Liver	Liver
9	chr5:1803000-1826000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:1803000-1826200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:1803000-1826200	Strong transcription	Adipose Nuclei	Adipose
12	chr5:1803000-1826600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr5:1803000-1826800	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:1803000-1827200	Strong transcription	Fetal Brain Female	brain
15	chr5:1803000-1828000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr5:1803200-1825600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr5:1803200-1825800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr5:1803200-1826800	Strong transcription	Primary T cells from cord blood	blood
19	chr5:1803600-1826800	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:1804000-1825000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:1804200-1824600	Weak transcription	Fetal Brain Male	brain
22	chr5:1808600-1825800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:1808800-1825000	Strong transcription	Brain Anterior Caudate	brain
24	chr5:1808800-1826200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr5:1808800-1826800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:1808800-1828800	Strong transcription	Dnd41	blood
27	chr5:1809400-1827800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr5:1809600-1824400	Strong transcription	NHEK	skin
29	chr5:1809800-1826800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:1809800-1828200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:1810000-1826600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:1811200-1825600	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:1813400-1826000	Strong transcription	Thymus	Thymus
34	chr5:1813600-1825200	Strong transcription	Brain Hippocampus Middle	brain
35	chr5:1813600-1826600	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr5:1813600-1827000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:1815000-1824600	Weak transcription	NHDF-Ad	bronchial
38	chr5:1816600-1828000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr5:1816800-1824800	Weak transcription	Stomach Mucosa	stomach
40	chr5:1817400-1826400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:1817800-1828000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:1818000-1828400	Weak transcription	Fetal Heart	heart
43	chr5:1819000-1826000	Strong transcription	Fetal Muscle Leg	muscle
44	chr5:1819400-1826800	Strong transcription	Fetal Intestine Small	intestine
45	chr5:1819400-1827000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:1819400-1828000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr5:1819600-1826600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:1820000-1828800	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr5:1820200-1827000	Strong transcription	Aorta	Aorta
50	chr5:1820400-1825200	Strong transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links