Variant report

Variant	rs12438686
Chromosome Location	chr15:52135292-52135293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52130556..52132790-chr15:52135069..52138067,2	MCF-7	breast:
2	chr15:52120473..52124016-chr15:52133834..52139102,7	K562	blood:
3	chr15:52132428..52137559-chr15:52138263..52141048,4	MCF-7	breast:
4	chr15:52105390..52107839-chr15:52134954..52136621,2	K562	blood:
5	chr15:52132092..52134106-chr15:52134200..52135846,2	MCF-7	breast:
6	chr15:52134932..52136622-chr15:52140952..52142810,2	K562	blood:
7	chr15:51913287..51915543-chr15:52134935..52137406,2	MCF-7	breast:
8	chr15:52129040..52133421-chr15:52134334..52139621,6	K562	blood:
9	chr15:52121368..52123870-chr15:52134346..52137266,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000104093	Chromatin interaction
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1025184	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs1035739	0.86[ASN][1000 genomes]
rs10444798	0.89[ASN][1000 genomes]
rs10444823	0.90[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs10775145	0.86[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs11630084	0.86[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs11632106	0.85[ASN][1000 genomes]
rs11636345	0.86[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs11638161	0.90[ASN][1000 genomes]
rs11638766	0.86[ASN][1000 genomes]
rs11638820	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12903707	0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs12905283	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs12917133	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1545602	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs17705732	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1811326	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1867984	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1895863	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1972689	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2009972	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs2034857	0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2034858	0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2052709	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs2241503	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs2252606	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs2253116	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs2264339	0.91[CHB][hapmap];0.96[JPT][hapmap];0.97[ASN][1000 genomes]
rs2414119	0.97[ASN][1000 genomes]
rs2436658	0.86[ASN][1000 genomes]
rs2436661	0.97[ASN][1000 genomes]
rs2470602	0.86[ASN][1000 genomes]
rs2470603	0.86[ASN][1000 genomes]
rs2470604	0.83[ASN][1000 genomes]
rs2470605	0.84[ASN][1000 genomes]
rs2470607	0.84[ASN][1000 genomes]
rs2470616	0.80[ASN][1000 genomes]
rs2470619	0.91[ASN][1000 genomes]
rs2554305	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2554306	0.97[ASN][1000 genomes]
rs2554307	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2554308	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2554315	0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2554334	0.94[ASN][1000 genomes]
rs2554336	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2554342	0.87[ASN][1000 genomes]
rs2554345	0.94[ASN][1000 genomes]
rs2554349	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs2554350	0.87[ASN][1000 genomes]
rs2570228	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2570231	0.97[ASN][1000 genomes]
rs2570233	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2570237	0.93[ASN][1000 genomes]
rs2570238	0.90[ASN][1000 genomes]
rs2570258	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2570260	0.94[ASN][1000 genomes]
rs2570263	0.85[ASN][1000 genomes]
rs2570268	0.88[ASN][1000 genomes]
rs2570269	0.86[ASN][1000 genomes]
rs2570271	0.86[ASN][1000 genomes]
rs2570275	0.87[ASN][1000 genomes]
rs2593167	0.82[ASN][1000 genomes]
rs2593173	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs2593179	0.86[ASN][1000 genomes]
rs2593183	0.88[ASN][1000 genomes]
rs2593185	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs2593187	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs2593191	0.94[ASN][1000 genomes]
rs2593198	0.87[ASN][1000 genomes]
rs2593202	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs2593204	0.86[ASN][1000 genomes]
rs2623254	0.91[CHB][hapmap];0.96[JPT][hapmap];0.96[ASN][1000 genomes]
rs2623262	0.94[ASN][1000 genomes]
rs2623279	0.88[ASN][1000 genomes]
rs2623281	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs2623283	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs2623286	0.87[ASN][1000 genomes]
rs2623288	0.88[ASN][1000 genomes]
rs2623289	0.86[ASN][1000 genomes]
rs2959302	0.83[ASN][1000 genomes]
rs3751596	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3794530	0.85[ASN][1000 genomes]
rs3794534	0.86[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs3794535	0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs3794536	0.97[ASN][1000 genomes]
rs4238383	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4502160	0.86[ASN][1000 genomes]
rs4534783	0.86[ASN][1000 genomes]
rs4774602	0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4775978	0.85[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4775982	0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4775983	0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs55843525	0.88[ASN][1000 genomes]
rs58758283	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59808035	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60329909	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6493518	0.86[ASN][1000 genomes]
rs6493519	0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs6493522	0.96[ASN][1000 genomes]
rs6493523	0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs689884	0.86[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs689922	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs690287	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs690638	0.91[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7162554	0.85[ASN][1000 genomes]
rs7165283	0.86[CHB][hapmap];0.96[JPT][hapmap]
rs7166110	0.85[ASN][1000 genomes]
rs7171459	0.97[ASN][1000 genomes]
rs7173375	0.85[ASN][1000 genomes]
rs7176421	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181553	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs72732952	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8024081	0.90[ASN][1000 genomes]
rs8024088	0.90[ASN][1000 genomes]
rs8024589	0.89[ASN][1000 genomes]
rs8026521	0.82[ASN][1000 genomes]
rs8028890	0.86[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs8041268	0.97[ASN][1000 genomes]
rs919059	0.94[ASN][1000 genomes]
rs9635308	0.91[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs990665	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2830255	chr15:52133914-52274863	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12438686	GNB5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52123600-52140000	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr15:52124200-52135400	Weak transcription	Thymus	Thymus
3	chr15:52125000-52137600	Weak transcription	Lung	lung
4	chr15:52129000-52136000	Enhancers	Fetal Lung	lung
5	chr15:52129000-52136600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr15:52129000-52140200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:52129200-52139800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr15:52129400-52140000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:52130000-52155000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:52130400-52137000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:52130400-52137600	Weak transcription	Placenta	Placenta
12	chr15:52130600-52135600	Weak transcription	Brain Anterior Caudate	brain
13	chr15:52130600-52136200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr15:52130800-52136400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:52130800-52137400	Weak transcription	Esophagus	oesophagus
16	chr15:52130800-52137600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:52130800-52155200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:52131000-52137800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:52131600-52137600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:52132200-52136800	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr15:52132200-52138000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr15:52132200-52140200	Enhancers	Primary T cells from cord blood	blood
23	chr15:52132400-52139400	Enhancers	Stomach Mucosa	stomach
24	chr15:52133000-52136000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr15:52133000-52136000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr15:52133000-52136600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:52133000-52143600	Enhancers	NHDF-Ad	bronchial
28	chr15:52133000-52146200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:52133200-52136200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:52133200-52137800	Enhancers	Fetal Intestine Large	intestine
31	chr15:52133200-52138000	Enhancers	Fetal Intestine Small	intestine
32	chr15:52133200-52139600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr15:52133200-52139800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr15:52133400-52137000	Enhancers	Primary B cells from cord blood	blood
35	chr15:52133600-52135800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr15:52133600-52136000	Enhancers	Adipose Nuclei	Adipose
37	chr15:52133600-52136400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr15:52133600-52136600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:52133600-52136600	Enhancers	Small Intestine	intestine
40	chr15:52133600-52138400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:52133600-52139400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:52133600-52139600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:52133600-52140000	Enhancers	HMEC	breast
44	chr15:52133800-52135600	Enhancers	Right Ventricle	heart
45	chr15:52133800-52136000	Enhancers	Primary B cells from peripheral blood	blood
46	chr15:52133800-52136000	Enhancers	Primary hematopoietic stem cells	blood
47	chr15:52133800-52136000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:52133800-52136200	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr15:52134000-52135400	Enhancers	Gastric	stomach
50	chr15:52134000-52135400	Enhancers	Pancreas	Pancrea

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