Variant report

Variant	rs489832
Chromosome Location	chr15:34277907-34277908
allele	A/G
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	CEBPB	chr15:34277504-34277907	IMR90	lung:	n/a	n/a
2	GATA3	chr15:34277408-34278313	SK-N-SH	brain:	n/a	chr15:34278148-34278159
3	PBX3	chr15:34277558-34277936	SK-N-SH	brain:	n/a	n/a
4	JUND	chr15:34277362-34278262	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr15:34277506-34278356	SK-N-SH	brain:	n/a	chr15:34278148-34278159
6	GATA3	chr15:34277698-34278327	MCF-7	breast:	n/a	chr15:34278148-34278159
7	TEAD4	chr15:34277595-34277963	ECC-1	luminal epithelium:	n/a	n/a
8	TEAD4	chr15:34277619-34277942	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr15:34277568-34278044	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr15:34277426-34278294	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000259505	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11856529	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12438680	0.81[ASN][1000 genomes]
rs12438682	0.82[ASN][1000 genomes]
rs16954030	0.86[ASN][1000 genomes]
rs2702281	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2702282	0.84[ASW][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28870091	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs478125	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5016373	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs511422	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs544114	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55805034	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs563663	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs569035	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56965184	0.83[ASN][1000 genomes]
rs588655	1.00[ASW][hapmap]
rs602807	0.86[EUR][1000 genomes]
rs603152	0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs604041	0.86[EUR][1000 genomes]
rs635531	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs636842	1.00[ASW][hapmap]
rs644585	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs646950	0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs6495419	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs6495421	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495422	1.00[CEU][hapmap];0.91[CHB][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495423	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495424	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495425	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495426	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8030334	0.81[GIH][hapmap];0.95[TSI][hapmap]
rs8035125	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]
rs8035294	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs8038713	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8039574	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs8039609	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043046	chr15:33714908-34321330	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1044844	chr15:34065524-34296829	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv456790	chr15:34264018-34281733	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv568923	chr15:34264018-34281733	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv2761666	chr15:34275262-34279231	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
9	nsv516347	chr15:34276169-34277907	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
10	nsv456791	chr15:34276169-34277907	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
11	nsv456792	chr15:34276169-34277907	Flanking Active TSS Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
12	nsv568924	chr15:34276169-34277907	Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs489832	PGBD4	cis	parietal	SCAN
rs489832	CHRM5	cis	cerebellum	SCAN
rs489832	CHRM5	cis	parietal	SCAN
rs489832	AVEN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34238000-34282400	Weak transcription	Ovary	ovary
2	chr15:34264800-34281200	Weak transcription	GM12878-XiMat	blood
3	chr15:34265200-34299600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:34265400-34294200	Weak transcription	Fetal Stomach	stomach
5	chr15:34265400-34311800	Weak transcription	Liver	Liver
6	chr15:34274400-34311000	Weak transcription	Primary B cells from cord blood	blood
7	chr15:34275400-34293200	Weak transcription	Primary T cells from cord blood	blood
8	chr15:34276800-34278200	Enhancers	Brain Cingulate Gyrus	brain
9	chr15:34276800-34278200	Enhancers	Brain Substantia Nigra	brain
10	chr15:34276800-34278400	Enhancers	Brain Hippocampus Middle	brain
11	chr15:34276800-34278400	Enhancers	Placenta	Placenta
12	chr15:34277000-34278000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:34277000-34278000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:34277000-34278000	Enhancers	Adipose Nuclei	Adipose
15	chr15:34277000-34278000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr15:34277000-34278200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr15:34277000-34278200	Enhancers	HSMMtube	muscle
18	chr15:34277200-34278000	Enhancers	H9 Cell Line	embryonic stem cell
19	chr15:34277200-34278000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:34277200-34278000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr15:34277200-34278000	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr15:34277200-34278000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:34277200-34278000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr15:34277200-34278000	Enhancers	Brain Anterior Caudate	brain
25	chr15:34277200-34278000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:34277200-34278000	Enhancers	Left Ventricle	heart
27	chr15:34277200-34278000	Enhancers	Rectal Smooth Muscle	rectum
28	chr15:34277200-34278200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:34277200-34278200	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr15:34277200-34278200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr15:34277200-34278200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:34277200-34278200	Enhancers	Brain Angular Gyrus	brain
33	chr15:34277200-34278200	Enhancers	NH-A	brain
34	chr15:34277200-34278400	Enhancers	HSMM	muscle
35	chr15:34277400-34278000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr15:34277400-34278000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr15:34277400-34278000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr15:34277400-34278000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:34277400-34278000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr15:34277400-34278000	Enhancers	NHDF-Ad	bronchial
41	chr15:34277400-34278000	Enhancers	NHLF	lung
42	chr15:34277400-34278200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:34277400-34278200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:34277400-34291200	Weak transcription	Aorta	Aorta
45	chr15:34277600-34278000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:34277600-34278000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:34277600-34278000	Enhancers	Fetal Heart	heart
48	chr15:34277600-34278000	Enhancers	NHEK	skin
49	chr15:34277600-34278200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:34277600-34279400	Weak transcription	HepG2	liver

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