Variant report

Variant	rs12903539
Chromosome Location	chr15:52486928-52486929
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	chr15:52485700..52488644-chr15:52493368..52494884,2	MCF-7	breast:
2	chr15:52486663..52491950-chr15:52497424..52502756,7	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1077383	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070882	0.87[AMR][1000 genomes]
rs11855672	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856177	0.82[AMR][1000 genomes]
rs12593936	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12593939	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12595160	0.84[AMR][1000 genomes]
rs12910398	1.00[YRI][hapmap]
rs12916135	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34276836	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35712143	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs35827106	0.87[AMR][1000 genomes]
rs4774612	0.86[ASN][1000 genomes]
rs4776010	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4776011	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4776013	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4776014	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66566761	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs66757864	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67163040	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs67447954	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs71472930	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7164508	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172037	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7183278	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8025737	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12903539	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 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	chr15:52474600-52488400	Weak transcription	Fetal Muscle Leg	muscle
8	chr15:52475800-52505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr15:52477600-52497000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr15:52477600-52497200	Weak transcription	Stomach Mucosa	stomach
11	chr15:52477800-52488000	Weak transcription	Gastric	stomach
12	chr15:52477800-52494800	Weak transcription	Fetal Intestine Large	intestine
13	chr15:52478000-52496200	Weak transcription	Liver	Liver
14	chr15:52478600-52488400	Weak transcription	Aorta	Aorta
15	chr15:52479600-52487400	Weak transcription	HepG2	liver
16	chr15:52479600-52495400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr15:52479600-52496400	Weak transcription	Esophagus	oesophagus
18	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
19	chr15:52481600-52496600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:52482600-52496200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr15:52483400-52492400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr15:52483600-52488400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:52483600-52489200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr15:52483600-52496400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:52483800-52487200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr15:52483800-52487200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:52483800-52487400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:52483800-52487800	Weak transcription	Colonic Mucosa	Colon
29	chr15:52483800-52488400	Weak transcription	Fetal Stomach	stomach
30	chr15:52483800-52497000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:52484000-52492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:52484200-52488200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:52484200-52488200	Weak transcription	Fetal Intestine Small	intestine
34	chr15:52484200-52488400	Weak transcription	Pancreas	Pancrea
35	chr15:52484200-52490600	Weak transcription	A549	lung
36	chr15:52484200-52496400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:52484200-52497000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:52484200-52498600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:52484200-52503200	Weak transcription	Lung	lung
40	chr15:52484400-52487200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr15:52484400-52503800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:52485600-52487400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:52485600-52488400	Weak transcription	Fetal Kidney	kidney
44	chr15:52485600-52489600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:52485800-52489400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:52485800-52489600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:52485800-52489800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:52486000-52487000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:52486000-52488000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:52486000-52496400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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