Variant report

Variant	rs4462564
Chromosome Location	chr15:39719780-39719781
allele	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	GATA2	chr15:39719693-39720285	SH-SY5Y	brain:	n/a	chr15:39720083-39720104 chr15:39720090-39720097 chr15:39720090-39720097 chr15:39720090-39720097
2	USF1	chr15:39719481-39719805	K562	blood:	n/a	n/a
3	POU2F2	chr15:39719182-39719847	GM12891	blood:	n/a	n/a
4	CHD2	chr15:39719195-39719815	GM12878	blood:	n/a	n/a
5	RELA	chr15:39719158-39719955	GM19099	blood:	n/a	n/a
6	POLR2A	chr15:39719199-39719872	HL-60	blood:	n/a	n/a
7	CEBPB	chr15:39719418-39719845	IMR90	lung:	n/a	chr15:39719710-39719721
8	MYC	chr15:39718988-39720326	NB4	blood:	n/a	n/a
9	PAX5	chr15:39719176-39719813	GM12878	blood:	n/a	n/a
10	BHLHE40	chr15:39719077-39719993	GM12878	blood:	n/a	n/a
11	ATF2	chr15:39719284-39719792	GM12878	blood:	n/a	n/a
12	WRNIP1	chr15:39719159-39720049	GM12878	blood:	n/a	n/a
13	ATF2	chr15:39719232-39719822	GM12878	blood:	n/a	n/a
14	CEBPB	chr15:39719552-39720353	K562	blood:	n/a	chr15:39719710-39719721
15	EP300	chr15:39719262-39719819	GM12878	blood:	n/a	n/a
16	NFATC1	chr15:39719195-39719819	GM12878	blood:	n/a	n/a
17	NFIC	chr15:39719213-39719815	GM12878	blood:	n/a	n/a
18	USF1	chr15:39719472-39719786	SK-N-SH_RA	brain:	n/a	n/a
19	MAX	chr15:39719288-39719788	GM12878	blood:	n/a	n/a
20	RAD21	chr15:39719456-39719830	SK-N-SH_RA	brain:	n/a	n/a
21	BHLHE40	chr15:39719389-39719800	K562	blood:	n/a	n/a
22	MAX	chr15:39719143-39720338	NB4	blood:	n/a	n/a
23	USF2	chr15:39719260-39719804	GM12878	blood:	n/a	n/a
24	STAT3	chr15:39719155-39719780	GM12878	blood:	n/a	chr15:39719654-39719665 chr15:39719656-39719664 chr15:39719653-39719667
25	NFIC	chr15:39719190-39719784	GM12878	blood:	n/a	n/a
26	FOXM1	chr15:39719142-39719935	GM12878	blood:	n/a	n/a
27	STAT3	chr15:39719439-39719838	MCF10A-Er-Src	breast:	n/a	chr15:39719654-39719665 chr15:39719656-39719664 chr15:39719653-39719667
28	MXI1	chr15:39719073-39720489	IMR90	lung:	n/a	n/a
29	TEAD4	chr15:39719432-39719863	K562	blood:	n/a	n/a
30	ETS1	chr15:39719428-39719784	GM12878	blood:	n/a	n/a
31	MYC	chr15:39719546-39719794	MCF10A-Er-Src	breast:	n/a	n/a
32	BCLAF1	chr15:39719224-39719849	GM12878	blood:	n/a	n/a
33	ZNF143	chr15:39719165-39719834	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:39719159-39719898	GM12892	blood:	n/a	n/a
35	SPI1	chr15:39718818-39719781	HL-60	blood:	n/a	chr15:39719109-39719118 chr15:39719106-39719119 chr15:39719107-39719120 chr15:39719110-39719117
36	CTCF	chr15:39719513-39719838	GM12878	blood:	n/a	n/a
37	STAT3	chr15:39719495-39719837	MCF10A-Er-Src	breast:	n/a	chr15:39719654-39719665 chr15:39719656-39719664 chr15:39719653-39719667
38	POLR2A	chr15:39719260-39719926	HL-60	blood:	n/a	n/a
39	RUNX3	chr15:39719069-39719836	GM12878	blood:	n/a	n/a
40	MTA3	chr15:39719147-39719936	GM12878	blood:	n/a	n/a
41	RUNX3	chr15:39719057-39719899	GM12878	blood:	n/a	n/a
42	IRF4	chr15:39719273-39719820	GM12878	blood:	n/a	n/a
43	STAT3	chr15:39719464-39719858	MCF10A-Er-Src	breast:	n/a	chr15:39719654-39719665 chr15:39719656-39719664 chr15:39719653-39719667
44	MAX	chr15:39719340-39719836	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000259345	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11631986	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12907034	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4244570	0.83[AFR][1000 genomes]
rs4417529	0.83[AFR][1000 genomes]
rs4533261	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4622487	0.86[AFR][1000 genomes]
rs4924350	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7182023	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8038785	0.87[AFR][1000 genomes]
rs8040081	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8040790	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920130	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1042824	chr15:39676039-39757222	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv542362	chr15:39676039-39757222	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1052908	chr15:39692049-39750193	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1044082	chr15:39693241-39750193	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1036091	chr15:39699841-39750193	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4462564	RP11-624L4.1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39712600-39724200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:39713000-39721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:39713200-39727400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:39718600-39720200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:39718800-39720000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:39718800-39720000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr15:39718800-39720000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:39718800-39720000	Enhancers	Right Atrium	heart
9	chr15:39718800-39720000	Flanking Active TSS	GM12878-XiMat	blood
10	chr15:39718800-39720200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:39718800-39720200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr15:39718800-39720200	Enhancers	Lung	lung
13	chr15:39718800-39720200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr15:39718800-39720400	Enhancers	Dnd41	blood
15	chr15:39718800-39720600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:39718800-39720600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr15:39719000-39719800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr15:39719000-39719800	Active TSS	Stomach Smooth Muscle	stomach
19	chr15:39719000-39719800	Flanking Active TSS	HSMMtube	muscle
20	chr15:39719000-39719800	Flanking Active TSS	Osteobl	bone
21	chr15:39719000-39720000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:39719000-39720000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr15:39719000-39720000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:39719000-39720200	Enhancers	Fetal Muscle Leg	muscle
25	chr15:39719000-39720400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr15:39719000-39720800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr15:39719000-39721600	Enhancers	Fetal Lung	lung
28	chr15:39719200-39719800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:39719200-39719800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:39719200-39719800	Active TSS	Primary B cells from cord blood	blood
31	chr15:39719200-39719800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr15:39719200-39719800	Active TSS	Brain Anterior Caudate	brain
33	chr15:39719200-39719800	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr15:39719200-39719800	Active TSS	Fetal Brain Female	brain
35	chr15:39719200-39719800	Enhancers	Stomach Mucosa	stomach
36	chr15:39719200-39719800	Active TSS	NHDF-Ad	bronchial
37	chr15:39719200-39720200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:39719200-39720200	Enhancers	Adipose Nuclei	Adipose
39	chr15:39719200-39720200	Enhancers	Fetal Heart	heart
40	chr15:39719200-39720200	Enhancers	Fetal Stomach	stomach
41	chr15:39719200-39720400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:39719200-39720400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr15:39719200-39721200	Enhancers	HepG2	liver
44	chr15:39719200-39723200	Enhancers	Left Ventricle	heart
45	chr15:39719200-39728200	Enhancers	HUVEC	blood vessel
46	chr15:39719400-39719800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:39719400-39719800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr15:39719400-39719800	Active TSS	Brain Angular Gyrus	brain
49	chr15:39719400-39719800	Active TSS	Duodenum Mucosa	Duodenum
50	chr15:39719400-39719800	Active TSS	Thymus	Thymus

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