Variant report

Variant	rs3751608
Chromosome Location	chr15:52505563-52505564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1011050	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1011051	0.86[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs11070884	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632093	0.90[AMR][1000 genomes]
rs11632174	0.84[ASN][1000 genomes]
rs11632189	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11638716	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11857447	0.88[AMR][1000 genomes]
rs2278295	0.86[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2414131	0.84[AMR][1000 genomes]
rs28624115	0.84[AMR][1000 genomes]
rs2899485	0.84[GIH][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs3751604	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3751606	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3794548	0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs3794550	0.84[JPT][hapmap]
rs4776016	0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs4776017	0.86[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs55683973	0.83[AMR][1000 genomes]
rs55812735	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55814691	0.83[AMR][1000 genomes]
rs56032655	0.84[AMR][1000 genomes]
rs56292520	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59434591	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60170969	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6493546	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178411	0.90[AMR][1000 genomes]
rs8024577	0.84[CHB][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs8038456	0.84[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9228	0.84[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv904220	chr15:52485024-52526507	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv1851383	chr15:52501831-52534344	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1537	chr15:52502246-52537067	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3751608	MYO5A	cis	cerebellum	SCAN
rs3751608	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52473200-52513600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52473600-52512400	Weak transcription	Primary B cells from cord blood	blood
3	chr15:52475800-52505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
5	chr15:52486000-52505800	Weak transcription	Psoas Muscle	Psoas
6	chr15:52488600-52509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:52488800-52505600	Weak transcription	Fetal Kidney	kidney
8	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:52495600-52519000	Strong transcription	HepG2	liver
11	chr15:52497400-52509400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:52497400-52510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:52497400-52514600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:52497600-52508800	Weak transcription	Stomach Mucosa	stomach
16	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr15:52499000-52515600	Weak transcription	Left Ventricle	heart
18	chr15:52499200-52512600	Strong transcription	A549	lung
19	chr15:52500000-52512000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr15:52500000-52519000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr15:52500600-52509200	Weak transcription	Brain Anterior Caudate	brain
22	chr15:52500800-52507400	Weak transcription	HUVEC	blood vessel
23	chr15:52501200-52506000	Strong transcription	Fetal Stomach	stomach
24	chr15:52501200-52506400	Strong transcription	Gastric	stomach
25	chr15:52501200-52506800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:52501400-52506800	Strong transcription	Pancreas	Pancrea
27	chr15:52501400-52512400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr15:52501600-52506800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr15:52501600-52519000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:52501600-52532600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr15:52501800-52506800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:52501800-52528000	Weak transcription	Fetal Heart	heart
33	chr15:52502000-52519200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:52502000-52523800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:52502400-52507000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:52502400-52520200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:52502600-52519000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:52502800-52505800	Strong transcription	Adipose Nuclei	Adipose
39	chr15:52502800-52506800	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr15:52502800-52506800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr15:52502800-52517800	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:52503000-52505600	Strong transcription	Brain Hippocampus Middle	brain
43	chr15:52503000-52506200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:52503000-52506800	Strong transcription	Liver	Liver
45	chr15:52503000-52507000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr15:52503000-52507200	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:52503200-52505800	Strong transcription	Fetal Muscle Leg	muscle
48	chr15:52503200-52506000	Strong transcription	Spleen	Spleen
49	chr15:52503200-52506400	Strong transcription	Esophagus	oesophagus
50	chr15:52503200-52506400	Strong transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links