Variant report

Variant	rs7172037
Chromosome Location	chr15:52472273-52472274
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:223)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:223 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD2	chr15:52471557-52472479	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF12	chr15:52472083-52472439	GM12878	blood:	n/a	chr15:52472246-52472253
3	SP1	chr15:52471842-52472564	A549	lung:	n/a	chr15:52471935-52471947 chr15:52471936-52471945
4	POLR2A	chr15:52471409-52472817	GM12891	blood:	n/a	n/a
5	POLR2A	chr15:52471888-52472364	GM12891	blood:	n/a	n/a
6	MAX	chr15:52471488-52472365	K562	blood:	n/a	n/a
7	POLR2A	chr15:52471323-52472437	MCF10A-Er-Src	breast:	n/a	n/a
8	USF2	chr15:52472231-52472375	H1-hESC	embryonic stem cell:	n/a	chr15:52472246-52472262
9	TCF12	chr15:52471451-52472429	ECC-1	luminal epithelium:	n/a	chr15:52472246-52472253
10	POLR2A	chr15:52471469-52472414	PFSK-1	brain:	n/a	n/a
11	HDAC2	chr15:52470838-52472694	MCF-7	breast:	n/a	n/a
12	TBP	chr15:52471973-52472303	HepG2	liver:	n/a	n/a
13	CEBPB	chr15:52472114-52472350	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr15:52471914-52472431	HepG2	liver:	n/a	n/a
15	YY1	chr15:52471517-52472543	HepG2	liver:	n/a	chr15:52471844-52471858 chr15:52471725-52471734
16	PAX5	chr15:52471954-52472586	GM12878	blood:	n/a	chr15:52472256-52472265
17	TCF7L2	chr15:52471476-52472318	HCT-116	colon:	n/a	n/a
18	POLR2A	chr15:52471881-52472505	GM12891	blood:	n/a	n/a
19	POLR2A	chr15:52471251-52472524	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr15:52471499-52472482	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr15:52471437-52472450	U87	brain:	n/a	n/a
22	RCOR1	chr15:52471421-52472799	IMR90	lung:	n/a	n/a
23	POLR2A	chr15:52471437-52472674	H1-hESC	embryonic stem cell:	n/a	n/a
24	HDAC2	chr15:52471904-52472436	HepG2	liver:	n/a	n/a
25	JUND	chr15:52472086-52472320	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr15:52471857-52472486	SK-N-SH	brain:	n/a	n/a
27	BCLAF1	chr15:52471893-52472515	GM12878	blood:	n/a	chr15:52472244-52472257 chr15:52472217-52472230
28	YY1	chr15:52471883-52472339	GM12891	blood:	n/a	n/a
29	POLR2A	chr15:52471424-52472526	HepG2	liver:	n/a	n/a
30	POLR2A	chr15:52471487-52472566	MCF-7	breast:	n/a	n/a
31	MAX	chr15:52471498-52472395	H1-hESC	embryonic stem cell:	n/a	n/a
32	YY1	chr15:52471927-52472439	H1-hESC	embryonic stem cell:	n/a	n/a
33	ZNF143	chr15:52471983-52472542	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr15:52471427-52472425	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr15:52471371-52472427	HCT-116	colon:	n/a	n/a
36	HEY1	chr15:52471968-52472384	HepG2	liver:	n/a	chr15:52472216-52472231
37	POLR2A	chr15:52471933-52472417	HepG2	liver:	n/a	n/a
38	MYC	chr15:52471488-52472370	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr15:52471875-52472520	GM12892	blood:	n/a	n/a
40	POLR2A	chr15:52471524-52472379	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr15:52471503-52472417	A549	lung:	n/a	n/a
42	POLR2A	chr15:52471468-52472754	Raji	blood:	n/a	n/a
43	SMC3	chr15:52471428-52472375	Hela-S3	cervix:	n/a	n/a
44	STAT1	chr15:52471982-52472359	GM12878	blood:	n/a	n/a
45	MXI1	chr15:52471143-52472690	IMR90	lung:	n/a	n/a
46	MAX	chr15:52471419-52472600	HepG2	liver:	n/a	n/a
47	MAZ	chr15:52471369-52472734	GM12878	blood:	n/a	n/a
48	TAF1	chr15:52471856-52472326	GM12878	blood:	n/a	n/a
49	GTF2F1	chr15:52471472-52472291	H1-hESC	embryonic stem cell:	n/a	n/a
50	YY1	chr15:52471850-52472499	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52431760..52432518-chr15:52471657..52472610,2	MCF-7	breast:
2	chr15:52469254..52473137-chr15:52482082..52484822,3	MCF-7	breast:
3	chr15:52262628..52265811-chr15:52469801..52473537,4	MCF-7	breast:
4	chr10:102791922..102792646-chr15:52471759..52472591,2	Hela-S3	cervix:
5	chr15:52261233..52265470-chr15:52469433..52474401,7	MCF-7	breast:
6	chr15:52453475..52455065-chr15:52470814..52473297,2	MCF-7	breast:
7	chr15:52403961..52406655-chr15:52470750..52472609,2	MCF-7	breast:
8	chr15:52469891..52472535-chr7:101457623..101459859,2	MCF-7	breast:
9	chr15:52310228..52314421-chr15:52470196..52474583,10	MCF-7	breast:
10	chr15:52471606..52474393-chr15:52859715..52862487,2	MCF-7	breast:
11	chr15:52311211..52313546-chr15:52470591..52472771,2	MCF-7	breast:
12	chr15:52418174..52420901-chr15:52470720..52473128,3	MCF-7	breast:

No data

Variant related genes	Relation type
GNB5	TF binding region
ENSG00000259577	TF binding region
ENSG00000069956	Chromatin interaction
ENSG00000206995	Chromatin interaction
ENSG00000137875	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000257923	Chromatin interaction
ENSG00000107819	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1077383	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11070882	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11855672	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11856177	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12438743	0.81[AMR][1000 genomes]
rs12593936	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593939	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12595160	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12901730	0.81[AMR][1000 genomes]
rs12901891	0.81[AMR][1000 genomes]
rs12902073	0.81[AMR][1000 genomes]
rs12903539	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12903769	0.81[AMR][1000 genomes]
rs12916135	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34276836	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35712143	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35827106	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4774612	0.84[ASN][1000 genomes]
rs4776010	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776011	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776013	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4776014	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66566761	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67163040	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67447954	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67725996	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71472930	0.84[ASN][1000 genomes]
rs7164508	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7183278	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8025737	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7172037	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52470200-52472800	Active TSS	Brain Anterior Caudate	brain
2	chr15:52470600-52473000	Active TSS	Brain Angular Gyrus	brain
3	chr15:52470600-52473000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr15:52470600-52473400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:52470800-52472400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:52470800-52472400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:52470800-52472600	Active TSS	Brain Hippocampus Middle	brain
8	chr15:52470800-52473000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:52470800-52473000	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr15:52470800-52473200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:52471000-52472400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:52471000-52472600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:52471000-52472600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr15:52471000-52472600	Active TSS	Colon Smooth Muscle	Colon
15	chr15:52471000-52472800	Active TSS	Ovary	ovary
16	chr15:52471000-52473000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:52471000-52473000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:52471000-52473000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:52471000-52473000	Active TSS	Aorta	Aorta
20	chr15:52471000-52473000	Active TSS	Esophagus	oesophagus
21	chr15:52471200-52472400	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr15:52471200-52472400	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr15:52471200-52472400	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr15:52471200-52472400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:52471200-52472400	Active TSS	Fetal Brain Male	brain
26	chr15:52471200-52472400	Active TSS	Psoas Muscle	Psoas
27	chr15:52471200-52472600	Active TSS	H1 Cell Line	embryonic stem cell
28	chr15:52471200-52472600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:52471200-52472600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:52471200-52472600	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr15:52471200-52472600	Active TSS	Fetal Heart	heart
32	chr15:52471200-52472600	Active TSS	Lung	lung
33	chr15:52471200-52472600	Active TSS	Placenta Amnion	Placenta Amnion
34	chr15:52471200-52472800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr15:52471200-52472800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:52471200-52472800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:52471200-52472800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr15:52471200-52472800	Active TSS	Brain Substantia Nigra	brain
39	chr15:52471200-52472800	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr15:52471200-52472800	Active TSS	Gastric	stomach
41	chr15:52471200-52472800	Active TSS	Left Ventricle	heart
42	chr15:52471200-52472800	Active TSS	Pancreas	Pancrea
43	chr15:52471200-52472800	Active TSS	NHDF-Ad	bronchial
44	chr15:52471200-52473000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:52471200-52473000	Active TSS	Fetal Kidney	kidney
46	chr15:52471200-52473000	Active TSS	Right Ventricle	heart
47	chr15:52471200-52473200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:52471200-52473200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:52471200-52473200	Active TSS	Fetal Brain Female	brain
50	chr15:52471400-52472400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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