Variant report

Variant	rs3764189
Chromosome Location	chr15:76304642-76304643
allele	A/C/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	EGR1	chr15:76304521-76305039	ECC-1	luminal epithelium:	n/a	chr15:76304786-76304799
2	EGR1	chr15:76304629-76304876	K562	blood:	n/a	chr15:76304786-76304799
3	TCF12	chr15:76304410-76305114	A549	lung:	n/a	n/a
4	FOS	chr15:76304271-76304764	MCF10A-Er-Src	breast:	n/a	chr15:76304599-76304611 chr15:76304600-76304610 chr15:76304602-76304613 chr15:76304601-76304609
5	EGR1	chr15:76304616-76304974	K562	blood:	n/a	chr15:76304786-76304799
6	MAX	chr15:76304329-76305130	ECC-1	luminal epithelium:	n/a	n/a
7	RCOR1	chr15:76304501-76304890	K562	blood:	n/a	n/a
8	USF2	chr15:76304482-76305009	Hela-S3	cervix:	n/a	n/a
9	ZMIZ1	chr15:76304299-76304949	K562	blood:	n/a	n/a
10	MXI1	chr15:76304424-76305006	Hela-S3	cervix:	n/a	n/a
11	MAFK	chr15:76304138-76304907	Hela-S3	cervix:	n/a	n/a
12	JUND	chr15:76304387-76304943	K562	blood:	n/a	chr15:76304599-76304611 chr15:76304600-76304610 chr15:76304602-76304613 chr15:76304601-76304609
13	TCF12	chr15:76304400-76304970	ECC-1	luminal epithelium:	n/a	n/a
14	ESR1	chr15:76304573-76304961	ECC-1	luminal epithelium:	n/a	n/a
15	MAZ	chr15:76304516-76304854	K562	blood:	n/a	n/a
16	MAX	chr15:76304514-76305021	ECC-1	luminal epithelium:	n/a	n/a
17	TEAD4	chr15:76303925-76305060	ECC-1	luminal epithelium:	n/a	chr15:76304967-76304976
18	POLR2A	chr15:76304585-76304884	Hela-S3	cervix:	n/a	n/a
19	EP300	chr15:76304370-76305068	ECC-1	luminal epithelium:	n/a	n/a
20	ARID3A	chr15:76304405-76304909	K562	blood:	n/a	n/a
21	EP300	chr15:76304178-76305092	A549	lung:	n/a	n/a
22	TBP	chr15:76304019-76305082	Hela-S3	cervix:	n/a	n/a
23	MYC	chr15:76304434-76304956	K562	blood:	n/a	n/a
24	CEBPB	chr15:76303866-76304979	Hela-S3	cervix:	n/a	n/a
25	MAX	chr15:76304389-76304962	Hela-S3	cervix:	n/a	n/a
26	NR2F2	chr15:76304540-76304988	K562	blood:	n/a	n/a
27	MAFF	chr15:76304561-76304902	K562	blood:	n/a	n/a
28	TAL1	chr15:76304635-76304928	K562	blood:	n/a	n/a
29	EP300	chr15:76304382-76304923	K562	blood:	n/a	n/a
30	GTF3C2	chr15:76304028-76304774	Hela-S3	cervix:	n/a	n/a
31	SP1	chr15:76304434-76305063	A549	lung:	n/a	n/a
32	EGR1	chr15:76304603-76304925	ECC-1	luminal epithelium:	n/a	chr15:76304786-76304799
33	CUX1	chr15:76304346-76304781	K562	blood:	n/a	n/a
34	NR2F2	chr15:76304476-76305055	MCF-7	breast:	n/a	n/a
35	POLR2A	chr15:76304321-76304946	Hela-S3	cervix:	n/a	n/a
36	MAX	chr15:76304582-76304993	A549	lung:	n/a	n/a
37	MAX	chr15:76304472-76305080	A549	lung:	n/a	n/a
38	KAP1	chr15:76304339-76304899	U2OS	brain:	n/a	n/a
39	TEAD4	chr15:76304590-76305050	ECC-1	luminal epithelium:	n/a	chr15:76304967-76304976
40	POLR2A	chr15:76304393-76304903	Hela-S3	cervix:	n/a	n/a
41	BACH1	chr15:76304558-76304885	K562	blood:	n/a	n/a
42	TBL1XR1	chr15:76304367-76304902	K562	blood:	n/a	n/a
43	ESR1	chr15:76304586-76304923	ECC-1	luminal epithelium:	n/a	n/a
44	ESR1	chr15:76304636-76304940	ECC-1	luminal epithelium:	n/a	n/a
45	TBP	chr15:76304447-76304901	K562	blood:	n/a	n/a
46	RFX5	chr15:76304062-76305406	Hela-S3	cervix:	n/a	n/a
47	FOSL2	chr15:76304324-76304878	A549	lung:	n/a	chr15:76304599-76304611 chr15:76304600-76304610 chr15:76304602-76304613 chr15:76304601-76304609
48	POLR2A	chr15:76303857-76305008	Hela-S3	cervix:	n/a	n/a
49	BHLHE40	chr15:76304627-76304947	A549	lung:	n/a	n/a
50	EP300	chr15:76304589-76305000	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:98909260..98909777-chr15:76304548..76305292,2	Hela-S3	cervix:

Variant related genes	Relation type
NRG4	TF binding region
ENSG00000120802	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11636891	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs11638364	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12899204	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12909182	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12910038	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12910494	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12911337	0.82[ASW][hapmap];0.92[LWK][hapmap]
rs12913434	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12915152	0.84[EUR][1000 genomes]
rs1499063	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17427165	0.84[EUR][1000 genomes]
rs17427298	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17427842	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2441930	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs35031760	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35656041	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62027608	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62027611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62027652	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62028932	0.84[EUR][1000 genomes]
rs62028936	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72734564	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72734574	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[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	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1053717	chr15:76196674-76314542	Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1040053	chr15:76197988-76314542	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904398	chr15:76220285-76359055	Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3764189	NRG4	cis	parietal	SCAN
rs3764189	FBXO22	cis	parietal	SCAN
rs3764189	ODF3L1	cis	parietal	SCAN
rs3764189	ETFA	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76302800-76304800	Active TSS	Hela-S3	cervix
2	chr15:76303000-76304800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:76303200-76305000	Active TSS	Stomach Mucosa	stomach
4	chr15:76303600-76305000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:76303800-76304800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:76303800-76305000	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr15:76303800-76305000	Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr15:76303800-76305200	Active TSS	A549	lung
9	chr15:76304000-76304800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr15:76304000-76304800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:76304000-76304800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
12	chr15:76304000-76304800	Active TSS	Fetal Stomach	stomach
13	chr15:76304000-76304800	Active TSS	Pancreas	Pancrea
14	chr15:76304000-76304800	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr15:76304000-76305000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:76304000-76305000	Active TSS	Aorta	Aorta
17	chr15:76304000-76305000	Active TSS	Psoas Muscle	Psoas
18	chr15:76304000-76305000	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr15:76304200-76304800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr15:76304200-76304800	Active TSS	K562	blood
21	chr15:76304200-76305000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr15:76304200-76305000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:76304400-76304800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:76304400-76304800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:76304400-76304800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:76304400-76304800	Enhancers	Colon Smooth Muscle	Colon
27	chr15:76304400-76304800	Enhancers	HSMM	muscle
28	chr15:76304400-76304800	Active TSS	Monocytes-CD14+_RO01746	blood
29	chr15:76304400-76304800	Flanking Bivalent TSS/Enh	Osteobl	bone
30	chr15:76304400-76305000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:76304400-76305000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:76304400-76305000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr15:76304400-76305000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:76304400-76305000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
35	chr15:76304400-76305000	Active TSS	Adipose Nuclei	Adipose
36	chr15:76304400-76305000	Active TSS	Rectal Smooth Muscle	rectum
37	chr15:76304400-76305000	Flanking Active TSS	HMEC	breast
38	chr15:76304400-76305000	Bivalent/Poised TSS	HSMMtube	muscle
39	chr15:76304600-76305000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:76304600-76305000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr15:76304600-76305000	Enhancers	Primary hematopoietic stem cells	blood
42	chr15:76304600-76305000	Enhancers	Placenta	Placenta
43	chr15:76304600-76305000	Enhancers	Ovary	ovary
44	chr15:76304600-76305000	Active TSS	Placenta Amnion	Placenta Amnion
45	chr15:76304600-76305000	Enhancers	Stomach Smooth Muscle	stomach
46	chr15:76304600-76305000	Flanking Active TSS	NHEK	skin

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