Variant report

Variant	rs2469560
Chromosome Location	chr15:76474260-76474261
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	ATF2	chr15:76473823-76474454	GM12878	blood:	n/a	n/a
2	CUX1	chr15:76474015-76474282	GM12878	blood:	n/a	n/a
3	NFIC	chr15:76473874-76474515	GM12878	blood:	n/a	n/a
4	RUNX3	chr15:76473810-76474499	GM12878	blood:	n/a	n/a
5	EBF1	chr15:76473925-76474424	GM12878	blood:	n/a	n/a
6	CHD2	chr15:76473975-76474412	GM12878	blood:	n/a	n/a
7	PAX5	chr15:76473978-76474307	GM12878	blood:	n/a	chr15:76474295-76474304
8	PAX5	chr15:76473885-76474575	GM12878	blood:	n/a	chr15:76474295-76474304
9	CREB1	chr15:76473855-76474574	GM12878	blood:	n/a	n/a
10	SP1	chr15:76473929-76474391	GM12878	blood:	n/a	n/a
11	NFATC1	chr15:76473848-76474351	GM12878	blood:	n/a	n/a
12	PAX5	chr15:76473941-76474401	GM12891	blood:	n/a	chr15:76474295-76474304
13	FOXM1	chr15:76473836-76474541	GM12878	blood:	n/a	chr15:76473977-76473985
14	PAX5	chr15:76473914-76474392	GM12878	blood:	n/a	chr15:76474295-76474304
15	EP300	chr15:76473962-76474394	GM12878	blood:	n/a	n/a
16	EP300	chr15:76474031-76474283	GM12878	blood:	n/a	n/a
17	SP1	chr15:76473843-76474414	GM12878	blood:	n/a	n/a
18	TBL1XR1	chr15:76473926-76474347	GM12878	blood:	n/a	n/a
19	FOXM1	chr15:76473760-76474490	GM12878	blood:	n/a	chr15:76473977-76473985
20	YY1	chr15:76473902-76474347	GM12878	blood:	n/a	n/a
21	SMC3	chr15:76474050-76474303	GM12878	blood:	n/a	n/a
22	ATF2	chr15:76473954-76474425	GM12878	blood:	n/a	n/a
23	PAX5	chr15:76473932-76474332	GM12878	blood:	n/a	chr15:76474295-76474304
24	TCF12	chr15:76474011-76474299	GM12878	blood:	n/a	n/a
25	MAX	chr15:76473981-76474419	GM12878	blood:	n/a	n/a
26	BCLAF1	chr15:76473905-76474445	GM12878	blood:	n/a	n/a
27	MEF2A	chr15:76473867-76474319	GM12878	blood:	n/a	n/a
28	RUNX3	chr15:76473764-76474592	GM12878	blood:	n/a	n/a
29	BCLAF1	chr15:76473788-76474517	GM12878	blood:	n/a	n/a
30	BCL11A	chr15:76474032-76474320	GM12878	blood:	n/a	n/a
31	STAT5A	chr15:76473792-76474473	GM12878	blood:	n/a	chr15:76474293-76474304
32	EP300	chr15:76474003-76474438	GM12878	blood:	n/a	n/a
33	MTA3	chr15:76473866-76474447	GM12878	blood:	n/a	n/a
34	WRNIP1	chr15:76473995-76474550	GM12878	blood:	n/a	n/a
35	BCL11A	chr15:76473914-76474363	GM12878	blood:	n/a	n/a
36	EGR1	chr15:76474075-76474295	GM12878	blood:	n/a	n/a
37	BATF	chr15:76473865-76474455	GM12878	blood:	n/a	chr15:76474119-76474130
38	STAT5A	chr15:76473899-76474332	GM12878	blood:	n/a	chr15:76474293-76474304
39	RCOR1	chr15:76473937-76474502	GM12878	blood:	n/a	n/a
40	IRF4	chr15:76473786-76474447	GM12878	blood:	n/a	n/a
41	MTA3	chr15:76473690-76474618	GM12878	blood:	n/a	n/a
42	GTF2F1	chr15:76474136-76474306	Hela-S3	cervix:	n/a	n/a
43	BHLHE40	chr15:76473924-76474330	GM12878	blood:	n/a	n/a
44	CHD1	chr15:76474037-76474475	GM12878	blood:	n/a	n/a
45	MXI1	chr15:76474016-76474286	GM12878	blood:	n/a	n/a
46	IKZF1	chr15:76473889-76474584	GM12878	blood:	n/a	n/a
47	JUND	chr15:76473623-76474586	GM12878	blood:	n/a	chr15:76474383-76474394 chr15:76474382-76474390 chr15:76473867-76473876
48	NFIC	chr15:76473834-76474456	GM12878	blood:	n/a	n/a
49	NFATC1	chr15:76473879-76474421	GM12878	blood:	n/a	n/a
50	BATF	chr15:76473923-76474319	GM12878	blood:	n/a	chr15:76474119-76474130

Variant related genes	Relation type
ENSG00000259422	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17352695	1.00[CHB][hapmap]
rs17458234	1.00[CHB][hapmap]
rs2469208	1.00[CHD][hapmap]
rs8042654	1.00[CHD][hapmap]
rs882791	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1048760	chr15:76334544-76496977	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1039595	chr15:76431374-76483342	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv1045860	chr15:76431374-76485536	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv1053643	chr15:76431374-76485966	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	nsv1052496	chr15:76432823-76484981	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv1036319	chr15:76432823-76489955	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv1035806	chr15:76435640-76483342	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv1047539	chr15:76435640-76485966	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv1042750	chr15:76435640-76490547	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv1054289	chr15:76437970-76485966	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv1035389	chr15:76444695-76483342	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
14	nsv1041435	chr15:76444695-76484981	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
15	nsv1046448	chr15:76444695-76485966	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	nsv1046099	chr15:76444695-76490547	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv1054300	chr15:76445689-76483342	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
18	nsv1044603	chr15:76445689-76484981	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
19	nsv1043026	chr15:76445689-76485966	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
20	nsv1040683	chr15:76454194-76483342	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
21	nsv1041619	chr15:76454194-76484981	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
22	nsv1046485	chr15:76454194-76485536	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
23	nsv1053572	chr15:76454194-76485966	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
24	nsv1049916	chr15:76454194-76490547	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
25	nsv1046563	chr15:76460462-76483342	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
26	nsv1053775	chr15:76460462-76485966	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
27	nsv1054713	chr15:76460462-76505906	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2469560	ETFA	cis	lymphoblastoid	seeQTL
rs2469560	NPTN	cis	parietal	SCAN
rs2469560	CD276	cis	parietal	SCAN
rs2469560	NRG4	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76443200-76483000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:76468000-76478000	Weak transcription	Pancreas	Pancrea
3	chr15:76470600-76482800	Weak transcription	A549	lung
4	chr15:76470800-76476000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:76470800-76476000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:76470800-76476200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:76471000-76475800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:76471000-76478000	Weak transcription	HMEC	breast
9	chr15:76471000-76478200	Weak transcription	Esophagus	oesophagus
10	chr15:76471000-76478200	Weak transcription	Hela-S3	cervix
11	chr15:76471200-76475000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:76471200-76476400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:76471400-76474400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:76471400-76482400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:76471600-76478200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:76472400-76478200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:76472600-76474400	Enhancers	HSMMtube	muscle
18	chr15:76472600-76475400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:76473200-76474600	Enhancers	Psoas Muscle	Psoas
20	chr15:76473400-76474600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:76473600-76474600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:76473600-76474600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:76473600-76474600	Flanking Active TSS	GM12878-XiMat	blood
24	chr15:76473600-76475200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:76473800-76474400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr15:76473800-76474400	Bivalent Enhancer	HepG2	liver
27	chr15:76473800-76475200	Enhancers	NHDF-Ad	bronchial
28	chr15:76473800-76475400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr15:76473800-76476200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:76473800-76477200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:76473800-76478200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:76474000-76474400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:76474000-76478200	Weak transcription	HSMM	muscle
34	chr15:76474200-76475600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:76474200-76479800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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