Variant report

Variant	rs3776152
Chromosome Location	chr5:1803164-1803165
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:1799223-1804902	K562	blood:	n/a	n/a

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:
4	chr5:1801625..1804390-chr5:1831978..1833592,2	K562	blood:

Variant related genes	Relation type
MRPL36	TF binding region
ENSG00000249116	Chromatin interaction
ENSG00000113430	Chromatin interaction
ENSG00000249326	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10074291	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10475109	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10866526	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11739312	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11740602	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740753	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11741881	0.95[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11748427	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11750565	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1546252	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1546253	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17535295	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17535337	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17535721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2131588	0.95[CEU][hapmap];0.92[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2131589	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2172530	0.86[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2353585	0.90[CEU][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3752844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3756344	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776154	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4147775	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4275010	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4277951	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4296838	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4296839	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4304110	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4416633	0.94[CEU][hapmap];0.92[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4588629	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60542979	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62336037	0.82[ASN][1000 genomes]
rs62338060	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62338061	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62338062	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6859338	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6862914	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6864281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6868515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6873986	0.95[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6880885	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6881253	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6890404	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6894566	0.95[CEU][hapmap];0.92[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7701970	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7703762	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7714300	0.80[EUR][1000 genomes];0.88[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
rs3776152	MRPL36	cis	multi-tissue	Pritchard
rs3776152	MRPL36	cis	Muscle Skeletal	GTEx
rs3776152	MRPL36	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1802000-1803400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:1802200-1803200	Weak transcription	Esophagus	oesophagus
3	chr5:1802200-1803200	Weak transcription	Stomach Mucosa	stomach
4	chr5:1802200-1803400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:1802200-1803400	Weak transcription	Aorta	Aorta
6	chr5:1802200-1805800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:1802200-1806400	Weak transcription	Small Intestine	intestine
8	chr5:1802200-1827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:1802400-1803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:1802400-1803200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:1802400-1803200	Weak transcription	Brain Substantia Nigra	brain
12	chr5:1802400-1803200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:1802400-1803200	Weak transcription	Thymus	Thymus
14	chr5:1802400-1803200	Weak transcription	HSMMtube	muscle
15	chr5:1802400-1803400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:1802400-1803400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr5:1802400-1803400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:1802400-1803400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:1802400-1803400	Weak transcription	Colonic Mucosa	Colon
20	chr5:1802400-1803400	Weak transcription	Fetal Brain Male	brain
21	chr5:1802400-1803400	Weak transcription	Fetal Stomach	stomach
22	chr5:1802400-1803400	Weak transcription	Pancreas	Pancrea
23	chr5:1802400-1803600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:1802400-1803800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:1802600-1803200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:1802600-1803200	Genic enhancers	Primary T cells from cord blood	blood
27	chr5:1802600-1803200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:1802600-1803200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr5:1802600-1803200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:1802600-1803200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:1802600-1803200	Weak transcription	Colon Smooth Muscle	Colon
32	chr5:1802600-1803200	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr5:1802600-1803200	Weak transcription	HUVEC	blood vessel
34	chr5:1802600-1803400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:1802600-1803400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr5:1802600-1803400	Weak transcription	Fetal Intestine Small	intestine
37	chr5:1802600-1803600	Genic enhancers	Hela-S3	cervix
38	chr5:1802600-1803800	Weak transcription	Right Atrium	heart
39	chr5:1802600-1805000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
40	chr5:1802600-1814400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr5:1802800-1803200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:1802800-1803200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr5:1802800-1803200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:1802800-1803200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:1802800-1803200	Genic enhancers	Brain Hippocampus Middle	brain
46	chr5:1802800-1803200	Genic enhancers	HMEC	breast
47	chr5:1802800-1803400	Transcr. at gene 5' and 3'	Dnd41	blood
48	chr5:1802800-1803400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
49	chr5:1802800-1803800	Strong transcription	Left Ventricle	heart
50	chr5:1802800-1803800	Genic enhancers	HepG2	liver

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