Variant report

Variant	rs60542979
Chromosome Location	chr5:1804931-1804932
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1803153..1805432-chr5:1831999..1834113,2	MCF-7	breast:
2	chr5:1793765..1806799-chr5:1879445..1889322,45	MCF-7	breast:
3	chr5:1796457..1805482-chr5:1878036..1885786,21	MCF-7	breast:

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

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10074291	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10475109	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10866526	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11739312	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11740602	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11740753	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11741881	0.86[EUR][1000 genomes]
rs11748427	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11750565	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1546252	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1546253	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17535295	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17535721	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131588	0.86[EUR][1000 genomes]
rs2131589	0.84[EUR][1000 genomes]
rs2172530	0.83[EUR][1000 genomes]
rs2353585	0.86[EUR][1000 genomes]
rs3752844	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3756344	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3776152	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3776154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4147775	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4275010	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4277951	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4296838	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4296839	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4304110	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4416633	0.86[EUR][1000 genomes]
rs4588629	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62336037	0.85[AFR][1000 genomes]
rs62338060	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62338061	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62338062	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6859338	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6862914	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6864281	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6868515	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6873986	0.86[EUR][1000 genomes]
rs6880885	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6881253	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6890404	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6894566	0.86[EUR][1000 genomes]
rs7701970	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7703762	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7714300	0.80[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
rs60542979	MRPL36	cis	Muscle Skeletal	GTEx
rs60542979	MRPL36	Cis_1M	lymphoblastoid	RTeQTL
rs60542979	MRPL36	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1802200-1805800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:1802200-1806400	Weak transcription	Small Intestine	intestine
3	chr5:1802200-1827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:1802600-1805000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
5	chr5:1802600-1814400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:1802800-1805200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
7	chr5:1802800-1807800	Strong transcription	HSMM	muscle
8	chr5:1802800-1808000	Strong transcription	NH-A	brain
9	chr5:1802800-1812800	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr5:1802800-1816000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:1802800-1817800	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:1802800-1818400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr5:1802800-1818600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:1802800-1818800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:1802800-1821800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:1802800-1821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:1802800-1822000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr5:1802800-1822800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:1802800-1823000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:1802800-1823600	Strong transcription	Primary B cells from cord blood	blood
21	chr5:1802800-1825000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:1802800-1825800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:1802800-1826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:1802800-1828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:1803000-1805200	Strong transcription	Primary hematopoietic stem cells	blood
26	chr5:1803000-1805200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:1803000-1805400	Strong transcription	Fetal Kidney	kidney
28	chr5:1803000-1805600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr5:1803000-1807600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:1803000-1807800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:1803000-1807800	Strong transcription	Brain Anterior Caudate	brain
32	chr5:1803000-1808400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:1803000-1809000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:1803000-1810000	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr5:1803000-1810400	Strong transcription	Brain Angular Gyrus	brain
36	chr5:1803000-1810400	Strong transcription	Rectal Smooth Muscle	rectum
37	chr5:1803000-1810600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:1803000-1811200	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr5:1803000-1811200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:1803000-1812600	Strong transcription	Fetal Lung	lung
41	chr5:1803000-1812800	Strong transcription	Ovary	ovary
42	chr5:1803000-1816200	Strong transcription	Lung	lung
43	chr5:1803000-1816800	Strong transcription	Fetal Intestine Large	intestine
44	chr5:1803000-1818200	Strong transcription	Fetal Muscle Leg	muscle
45	chr5:1803000-1818400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:1803000-1818400	Strong transcription	NHLF	lung
47	chr5:1803000-1822400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:1803000-1822400	Strong transcription	A549	lung
49	chr5:1803000-1822600	Strong transcription	Placenta	Placenta
50	chr5:1803000-1822800	Strong transcription	Primary monocytes fromperipheralblood	blood

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