Variant report

Variant	rs3751606
Chromosome Location	chr15:52497681-52497682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50387437..50389948-chr15:52496988..52498573,2	K562	blood:
2	chr15:52496666..52498415-chr15:52943182..52945600,2	MCF-7	breast:
3	chr15:52486663..52491950-chr15:52497424..52502756,7	MCF-7	breast:
4	chr15:52477453..52480086-chr15:52495513..52498158,2	K562	blood:

Variant related genes	Relation type
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1011050	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1011051	0.86[CHB][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070884	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632093	0.86[AMR][1000 genomes]
rs11632174	0.85[ASN][1000 genomes]
rs11632189	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11638716	0.81[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11857447	0.84[AMR][1000 genomes]
rs2278295	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2899485	0.80[GIH][hapmap];0.86[MEX][hapmap]
rs3751604	0.92[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3751608	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];0.86[ASN][1000 genomes]
rs3794550	0.84[JPT][hapmap]
rs4776016	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs4776017	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs55812735	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56292520	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59434591	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60170969	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493546	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178411	0.86[AMR][1000 genomes]
rs8024577	0.81[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs8038456	0.84[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9228	0.81[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3751606	GNB5	Cis_1M	lymphoblastoid	RTeQTL
rs3751606	GNB5	cis	multi-tissue	Pritchard
rs3751606	MYO5A	cis	cerebellum	SCAN

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	chr15:52484200-52498600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:52484200-52503200	Weak transcription	Lung	lung
7	chr15:52484400-52503800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:52486000-52505800	Weak transcription	Psoas Muscle	Psoas
9	chr15:52487400-52505200	Weak transcription	Thymus	Thymus
10	chr15:52488600-52509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:52488800-52505600	Weak transcription	Fetal Kidney	kidney
12	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:52490400-52503000	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:52494600-52499200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:52495400-52497800	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr15:52495400-52500600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr15:52495600-52519000	Strong transcription	HepG2	liver
19	chr15:52495800-52498600	Weak transcription	Right Atrium	heart
20	chr15:52495800-52499200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr15:52496000-52497800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:52496000-52498000	Strong transcription	Gastric	stomach
23	chr15:52496000-52498200	Strong transcription	Primary hematopoietic stem cells	blood
24	chr15:52496000-52498400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:52496000-52498400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:52496000-52498600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:52496000-52499000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr15:52496000-52500800	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:52496000-52505000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:52496200-52497800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:52496200-52497800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr15:52496200-52499200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:52496200-52500200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:52496200-52501600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:52496200-52505400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:52496400-52497800	Strong transcription	Pancreas	Pancrea
37	chr15:52496800-52498800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr15:52497200-52498800	Weak transcription	Aorta	Aorta
39	chr15:52497200-52505200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr15:52497400-52498000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
41	chr15:52497400-52498800	Weak transcription	Left Ventricle	heart
42	chr15:52497400-52499200	Weak transcription	A549	lung
43	chr15:52497400-52499800	Weak transcription	Brain Anterior Caudate	brain
44	chr15:52497400-52501000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:52497400-52503000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:52497400-52505000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:52497400-52509400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:52497400-52510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:52497400-52514600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain

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