Variant report

Variant	rs11070884
Chromosome Location	chr15:52501831-52501832
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52466781..52469103-chr15:52500146..52502200,2	MCF-7	breast:
2	chr15:52470561..52473090-chr15:52500221..52502576,3	MCF-7	breast:
3	chr15:52500850..52502666-chr15:52514026..52515788,2	MCF-7	breast:
4	chr15:52271043..52273593-chr15:52500641..52502378,2	MCF-7	breast:
5	chr15:52216346..52217850-chr15:52500229..52502926,2	MCF-7	breast:
6	chr15:52473218..52475845-chr15:52500048..52503534,3	MCF-7	breast:
7	chr15:52486663..52491950-chr15:52497424..52502756,7	MCF-7	breast:
8	chr15:52498552..52502035-chr15:52503246..52505472,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1011050	0.81[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1011051	0.81[ASW][hapmap];0.86[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632093	0.83[AMR][1000 genomes]
rs11632174	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11632189	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11638716	0.86[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11857447	0.83[AMR][1000 genomes]
rs2278295	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.82[ASN][1000 genomes]
rs3751604	0.92[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3751606	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]
rs3751608	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]
rs3794542	0.89[ASW][hapmap]
rs3794548	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3794550	0.84[JPT][hapmap]
rs4776016	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs4776017	0.91[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs55812735	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56292520	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59434591	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60170969	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493546	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7178411	0.83[AMR][1000 genomes]
rs8024577	0.84[CHB][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap]
rs8038456	0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9228	0.84[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11070884	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 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	chr15:52484200-52503200	Weak transcription	Lung	lung
6	chr15:52484400-52503800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:52486000-52505800	Weak transcription	Psoas Muscle	Psoas
8	chr15:52487400-52505200	Weak transcription	Thymus	Thymus
9	chr15:52488600-52509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:52488800-52505600	Weak transcription	Fetal Kidney	kidney
11	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:52490400-52503000	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:52495600-52519000	Strong transcription	HepG2	liver
15	chr15:52496000-52505000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:52496200-52505400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:52497200-52505200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:52497400-52503000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:52497400-52505000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:52497400-52509400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:52497400-52510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:52497400-52514600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:52497600-52502800	Weak transcription	Adipose Nuclei	Adipose
25	chr15:52497600-52503200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr15:52497600-52503200	Weak transcription	Esophagus	oesophagus
27	chr15:52497600-52503200	Weak transcription	Fetal Intestine Small	intestine
28	chr15:52497600-52503200	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:52497600-52503200	Weak transcription	Spleen	Spleen
30	chr15:52497600-52503400	Weak transcription	Fetal Intestine Large	intestine
31	chr15:52497600-52503600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:52497600-52503600	Weak transcription	Primary T cells from cord blood	blood
33	chr15:52497600-52503600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:52497600-52503600	Weak transcription	Colonic Mucosa	Colon
35	chr15:52497600-52504000	Weak transcription	Right Ventricle	heart
36	chr15:52497600-52508800	Weak transcription	Stomach Mucosa	stomach
37	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr15:52498400-52503000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:52498600-52502000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:52499000-52502800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr15:52499000-52503800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:52499000-52504400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:52499000-52505200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:52499000-52515600	Weak transcription	Left Ventricle	heart
45	chr15:52499200-52503000	Weak transcription	Liver	Liver
46	chr15:52499200-52512600	Strong transcription	A549	lung
47	chr15:52499600-52502000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:52500000-52512000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr15:52500000-52519000	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr15:52500200-52502000	Strong transcription	Duodenum Mucosa	Duodenum

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