Variant report

Variant	rs16964760
Chromosome Location	chr15:52488885-52488886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52486663..52491950-chr15:52497424..52502756,7	MCF-7	breast:
2	chr15:52487648..52490505-chr15:52490817..52493164,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16964751	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16964764	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17540546	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17540734	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17541016	0.84[TSI][hapmap]
rs17612637	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17612796	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2231289	1.00[AMR][1000 genomes]
rs2414134	0.83[GIH][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs35581121	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41277704	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41277706	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs41277712	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4776006	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4776018	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4776019	0.94[AMR][1000 genomes]
rs4776020	0.81[EUR][1000 genomes]
rs62016465	1.00[AMR][1000 genomes]
rs62016466	1.00[AMR][1000 genomes]
rs6493536	0.97[EUR][1000 genomes]
rs6493537	0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs7168334	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7177057	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7181736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73402856	0.82[EUR][1000 genomes]
rs73402857	0.90[EUR][1000 genomes]
rs74015635	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8024846	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8024892	0.82[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16964760	GNB5	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52473000-52489000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:52473200-52513600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:52473400-52496400	Weak transcription	Brain Anterior Caudate	brain
4	chr15:52473400-52496400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:52473400-52496600	Weak transcription	Spleen	Spleen
6	chr15:52473600-52512400	Weak transcription	Primary B cells from cord blood	blood
7	chr15:52475800-52505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:52477600-52497000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr15:52477600-52497200	Weak transcription	Stomach Mucosa	stomach
10	chr15:52477800-52494800	Weak transcription	Fetal Intestine Large	intestine
11	chr15:52478000-52496200	Weak transcription	Liver	Liver
12	chr15:52479600-52495400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:52479600-52496400	Weak transcription	Esophagus	oesophagus
14	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
15	chr15:52481600-52496600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:52482600-52496200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr15:52483400-52492400	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr15:52483600-52489200	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr15:52483600-52496400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr15:52483800-52497000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:52484000-52492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:52484200-52490600	Weak transcription	A549	lung
23	chr15:52484200-52496400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:52484200-52497000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:52484200-52498600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:52484200-52503200	Weak transcription	Lung	lung
27	chr15:52484400-52503800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:52485600-52489600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:52485800-52489400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr15:52485800-52489600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:52485800-52489800	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:52486000-52496400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:52486000-52505800	Weak transcription	Psoas Muscle	Psoas
34	chr15:52486200-52489200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:52486200-52489600	Strong transcription	Duodenum Mucosa	Duodenum
36	chr15:52486400-52496200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:52486600-52496600	Weak transcription	Adipose Nuclei	Adipose
38	chr15:52487200-52489600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:52487400-52489400	Strong transcription	HepG2	liver
40	chr15:52487400-52489600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr15:52487400-52496200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:52487400-52496800	Weak transcription	Left Ventricle	heart
43	chr15:52487400-52505200	Weak transcription	Thymus	Thymus
44	chr15:52487800-52489000	Strong transcription	Colonic Mucosa	Colon
45	chr15:52488000-52489000	Strong transcription	Gastric	stomach
46	chr15:52488000-52489200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:52488200-52491800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:52488400-52489200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:52488400-52489200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr15:52488400-52489400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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