Variant report

Variant	rs4776010
Chromosome Location	chr15:52472683-52472684
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	chr15:52471409-52472817	GM12891	blood:	n/a	n/a
2	HDAC2	chr15:52470838-52472694	MCF-7	breast:	n/a	n/a
3	RCOR1	chr15:52471421-52472799	IMR90	lung:	n/a	n/a
4	EP300	chr15:52472558-52472742	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:52471468-52472754	Raji	blood:	n/a	n/a
6	MXI1	chr15:52471143-52472690	IMR90	lung:	n/a	n/a
7	MAZ	chr15:52471369-52472734	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:52471381-52473065	GM12892	blood:	n/a	n/a
9	MAX	chr15:52471260-52472842	A549	lung:	n/a	n/a
10	POLR2A	chr15:52471472-52472884	GM12878	blood:	n/a	n/a
11	ELF1	chr15:52471475-52472835	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:52471525-52472708	GM10847	blood:	n/a	n/a
13	POU2F2	chr15:52472423-52472818	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:52471271-52472784	H1-neurons	neurons:	n/a	n/a
15	EBF1	chr15:52472617-52473013	GM12878	blood:	n/a	n/a
16	REST	chr15:52470917-52473151	H1-neurons	neurons:	n/a	chr15:52472267-52472280 chr15:52472270-52472283 chr15:52471435-52471445 chr15:52472209-52472222 chr15:52472217-52472227
17	POU2F2	chr15:52472138-52472896	GM12891	blood:	n/a	n/a
18	ZNF143	chr15:52472172-52472704	GM12878	blood:	n/a	n/a
19	RUNX3	chr15:52471413-52472841	GM12878	blood:	n/a	n/a
20	STAT5A	chr15:52471872-52472719	GM12878	blood:	n/a	n/a
21	TAF1	chr15:52472431-52472690	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:52471513-52472780	GM12892	blood:	n/a	n/a
23	MAX	chr15:52470923-52472813	MCF-7	breast:	n/a	n/a
24	RUNX3	chr15:52471468-52472789	GM12878	blood:	n/a	n/a
25	POLR2A	chr15:52471491-52472773	GM19099	blood:	n/a	n/a
26	CTBP2	chr15:52471204-52473040	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:52471290-52473152	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr15:52471877-52472719	GM12892	blood:	n/a	n/a
29	MTA3	chr15:52471908-52473264	GM12878	blood:	n/a	n/a
30	STAT1	chr15:52472661-52472755	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:52471256-52473108	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr15:52471447-52472697	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr15:52471406-52472795	GM12878	blood:	n/a	n/a
34	ZNF263	chr15:52471486-52472924	HEK293-T-REx	kidney:	n/a	n/a
35	POU2F2	chr15:52471876-52472795	GM12878	blood:	n/a	chr15:52472091-52472103
36	TCF12	chr15:52471842-52472828	A549	lung:	n/a	chr15:52472246-52472253
37	POLR2A	chr15:52471477-52472917	GM18951	blood:	n/a	n/a
38	YY1	chr15:52471472-52472821	GM12892	blood:	n/a	chr15:52471844-52471858 chr15:52471725-52471734
39	MAZ	chr15:52471263-52472997	IMR90	lung:	n/a	n/a
40	MXI1	chr15:52470639-52472782	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr15:52471469-52472859	GM12892	blood:	n/a	n/a
42	TAF1	chr15:52471229-52472958	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr15:52471368-52473003	GM18505	blood:	n/a	n/a
44	TBL1XR1	chr15:52471996-52472747	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:52471502-52472861	GM15510	blood:	n/a	n/a
46	JUND	chr15:52471414-52472719	A549	lung:	n/a	chr15:52471942-52471951 chr15:52471938-52471947
47	ZEB1	chr15:52471509-52472750	GM12878	blood:	n/a	chr15:52471807-52471814 chr15:52472246-52472257
48	POU2F2	chr15:52472201-52472844	GM12891	blood:	n/a	n/a
49	POLR2A	chr15:52471494-52472764	GM18526	blood:	n/a	n/a
50	POLR2A	chr15:52471889-52472769	GM12878	blood:	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	chr15:52311211..52313546-chr15:52470591..52472771,2	MCF-7	breast:
10	chr15:52418174..52420901-chr15:52470720..52473128,3	MCF-7	breast:

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

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1077383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11070882	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11855672	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11856177	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12438743	0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs12593936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12593939	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595160	0.91[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];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]
rs12902522	1.00[CEU][hapmap]
rs12903539	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12903769	0.81[AMR][1000 genomes]
rs12909161	0.80[MEX][hapmap]
rs12916135	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16964750	0.83[AFR][1000 genomes]
rs2398	0.80[MEX][hapmap]
rs34276836	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35712143	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35827106	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3794543	0.80[MEX][hapmap]
rs4774612	1.00[CHB][hapmap];0.89[GIH][hapmap];0.82[ASN][1000 genomes]
rs4776011	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776013	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776014	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59289747	0.81[AFR][1000 genomes]
rs66566761	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67163040	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67447954	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67725996	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71472930	0.82[ASN][1000 genomes]
rs7164508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165708	0.82[AFR][1000 genomes]
rs7172037	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7183278	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404813	0.84[AFR][1000 genomes]
rs8024311	0.81[AFR][1000 genomes]
rs8025737	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8040458	0.83[AFR][1000 genomes]
rs8041504	0.81[AFR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4776010	LEO1	cis	parietal	SCAN
rs4776010	BCL2L10	cis	parietal	SCAN
rs4776010	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr15:52470800-52473000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:52470800-52473000	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr15:52470800-52473200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:52471000-52472800	Active TSS	Ovary	ovary
9	chr15:52471000-52473000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr15:52471000-52473000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:52471000-52473000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:52471000-52473000	Active TSS	Aorta	Aorta
13	chr15:52471000-52473000	Active TSS	Esophagus	oesophagus
14	chr15:52471200-52472800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr15:52471200-52472800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:52471200-52472800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:52471200-52472800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr15:52471200-52472800	Active TSS	Brain Substantia Nigra	brain
19	chr15:52471200-52472800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr15:52471200-52472800	Active TSS	Gastric	stomach
21	chr15:52471200-52472800	Active TSS	Left Ventricle	heart
22	chr15:52471200-52472800	Active TSS	Pancreas	Pancrea
23	chr15:52471200-52472800	Active TSS	NHDF-Ad	bronchial
24	chr15:52471200-52473000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:52471200-52473000	Active TSS	Fetal Kidney	kidney
26	chr15:52471200-52473000	Active TSS	Right Ventricle	heart
27	chr15:52471200-52473200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:52471200-52473200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:52471200-52473200	Active TSS	Fetal Brain Female	brain
30	chr15:52471400-52472800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:52471400-52472800	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr15:52471400-52472800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr15:52471400-52472800	Active TSS	Duodenum Mucosa	Duodenum
34	chr15:52471400-52472800	Active TSS	Rectal Smooth Muscle	rectum
35	chr15:52471400-52472800	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr15:52471400-52472800	Active TSS	Small Intestine	intestine
37	chr15:52471400-52472800	Active TSS	Stomach Mucosa	stomach
38	chr15:52471400-52473000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:52471400-52473000	Active TSS	HSMM	muscle
40	chr15:52471600-52472800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:52471600-52473000	Active TSS	Thymus	Thymus
42	chr15:52471600-52473000	Active TSS	NH-A	brain
43	chr15:52472000-52473000	Flanking Active TSS	Colonic Mucosa	Colon
44	chr15:52472000-52473200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:52472000-52473400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
46	chr15:52472200-52472800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:52472200-52472800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
48	chr15:52472200-52472800	Flanking Active TSS	Placenta	Placenta
49	chr15:52472200-52472800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
50	chr15:52472200-52472800	Flanking Active TSS	Dnd41	blood

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