Variant report

Variant	rs4776012
Chromosome Location	chr15:52472955-52472956
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52471381-52473065	GM12892	blood:	n/a	n/a
2	EBF1	chr15:52472617-52473013	GM12878	blood:	n/a	n/a
3	REST	chr15:52470917-52473151	H1-neurons	neurons:	n/a	chr15:52472267-52472280 chr15:52472270-52472283 chr15:52471435-52471445 chr15:52472209-52472222 chr15:52472217-52472227
4	CTBP2	chr15:52471204-52473040	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr15:52471290-52473152	H1-hESC	embryonic stem cell:	n/a	n/a
6	MTA3	chr15:52471908-52473264	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:52471256-52473108	H1-neurons	neurons:	n/a	n/a
8	MAZ	chr15:52471263-52472997	IMR90	lung:	n/a	n/a
9	TAF1	chr15:52471229-52472958	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr15:52471368-52473003	GM18505	blood:	n/a	n/a
11	SIN3A	chr15:52471215-52473121	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52469254..52473137-chr15:52482082..52484822,3	MCF-7	breast:
2	chr15:52262628..52265811-chr15:52469801..52473537,4	MCF-7	breast:
3	chr15:52261233..52265470-chr15:52469433..52474401,7	MCF-7	breast:
4	chr15:52453475..52455065-chr15:52470814..52473297,2	MCF-7	breast:
5	chr15:52472583..52475505-chr15:52484496..52486835,2	MCF-7	breast:
6	chr15:52472278..52474319-chr15:52482944..52484455,2	K562	blood:
7	chr15:52310228..52314421-chr15:52470196..52474583,10	MCF-7	breast:
8	chr15:52471606..52474393-chr15:52859715..52862487,2	MCF-7	breast:
9	chr15:52418174..52420901-chr15:52470720..52473128,3	MCF-7	breast:

Variant related genes	Relation type
GNB5	TF binding region
ENSG00000166477	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000206995	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12594679	0.91[EUR][1000 genomes]
rs12594809	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12898389	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12904880	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12910870	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12916557	0.91[EUR][1000 genomes]
rs34283892	0.90[EUR][1000 genomes]
rs35733550	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35914910	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4506834	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776008	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66757864	0.96[ASN][1000 genomes]
rs67725996	0.98[ASN][1000 genomes]
rs7166799	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7177248	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7181580	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8029782	0.91[AMR][1000 genomes];0.94[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	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4776012	BCL2L10	Cis_1M	lymphoblastoid	RTeQTL
rs4776012	GNB5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52470600-52473000	Active TSS	Brain Angular Gyrus	brain
2	chr15:52470600-52473000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr15:52470600-52473400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:52470800-52473000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:52470800-52473000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr15:52470800-52473200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:52471000-52473000	Active TSS	H9 Cell Line	embryonic stem cell
8	chr15:52471000-52473000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:52471000-52473000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:52471000-52473000	Active TSS	Aorta	Aorta
11	chr15:52471000-52473000	Active TSS	Esophagus	oesophagus
12	chr15:52471200-52473000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:52471200-52473000	Active TSS	Fetal Kidney	kidney
14	chr15:52471200-52473000	Active TSS	Right Ventricle	heart
15	chr15:52471200-52473200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:52471200-52473200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:52471200-52473200	Active TSS	Fetal Brain Female	brain
18	chr15:52471400-52473000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:52471400-52473000	Active TSS	HSMM	muscle
20	chr15:52471600-52473000	Active TSS	Thymus	Thymus
21	chr15:52471600-52473000	Active TSS	NH-A	brain
22	chr15:52472000-52473000	Flanking Active TSS	Colonic Mucosa	Colon
23	chr15:52472000-52473200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:52472000-52473400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr15:52472200-52473000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr15:52472200-52473000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:52472200-52473000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr15:52472200-52473000	Flanking Active TSS	HMEC	breast
29	chr15:52472200-52473000	Flanking Active TSS	HUVEC	blood vessel
30	chr15:52472200-52473000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
31	chr15:52472200-52473200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr15:52472200-52473200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr15:52472200-52473200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:52472200-52473400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:52472400-52473000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:52472400-52473000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
37	chr15:52472400-52473000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:52472400-52473000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:52472400-52473000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr15:52472400-52473000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr15:52472400-52473000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr15:52472400-52473000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
43	chr15:52472400-52473000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
44	chr15:52472400-52473000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
45	chr15:52472400-52473000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
46	chr15:52472400-52473000	Flanking Active TSS	Osteobl	bone
47	chr15:52472400-52473200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr15:52472400-52473200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
49	chr15:52472400-52473200	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr15:52472400-52473200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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