Variant report

Variant	rs3784389
Chromosome Location	chr15:59978920-59978921
allele	C/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	MAX	chr15:59978514-59979041	NB4	blood:	n/a	chr15:59978856-59978866 chr15:59978855-59978866
2	MYC	chr15:59978555-59979013	NB4	blood:	n/a	chr15:59978856-59978866 chr15:59978855-59978866
3	SPI1	chr15:59978566-59979012	HL-60	blood:	n/a	chr15:59978750-59978759 chr15:59978746-59978755 chr15:59978749-59978762 chr15:59978748-59978761
4	EBF1	chr15:59978542-59978985	GM12878	blood:	n/a	n/a
5	NFIC	chr15:59978476-59978949	GM12878	blood:	n/a	n/a
6	SIN3A	chr15:59978705-59978945	GM12878	blood:	n/a	n/a
7	EBF1	chr15:59978236-59979025	GM12878	blood:	n/a	n/a
8	SPI1	chr15:59978275-59979066	GM12878	blood:	n/a	chr15:59978750-59978759 chr15:59978746-59978755 chr15:59978749-59978762 chr15:59978748-59978761
9	MXI1	chr15:59978566-59979074	GM12878	blood:	n/a	n/a
10	REST	chr15:59978608-59978923	Hela-S3	cervix:	n/a	n/a
11	RUNX3	chr15:59978537-59978930	GM12878	blood:	n/a	n/a
12	SPI1	chr15:59978523-59978964	GM12878	blood:	n/a	chr15:59978750-59978759 chr15:59978746-59978755 chr15:59978749-59978762 chr15:59978748-59978761
13	SPI1	chr15:59978480-59978970	HL-60	blood:	n/a	chr15:59978750-59978759 chr15:59978746-59978755 chr15:59978749-59978762 chr15:59978748-59978761
14	EP300	chr15:59978441-59978925	GM12878	blood:	n/a	chr15:59978746-59978760
15	POLR2A	chr15:59978401-59979000	GM12878	blood:	n/a	n/a
16	SPI1	chr15:59978456-59978944	GM12891	blood:	n/a	chr15:59978750-59978759 chr15:59978746-59978755 chr15:59978749-59978762 chr15:59978748-59978761
17	EBF1	chr15:59978518-59978934	GM12878	blood:	n/a	n/a
18	SPI1	chr15:59978465-59978981	GM12891	blood:	n/a	chr15:59978750-59978759 chr15:59978746-59978755 chr15:59978749-59978762 chr15:59978748-59978761
19	MTA3	chr15:59978349-59979000	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
2	chr15:59975789..59979387-chr15:59979488..59982275,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259238	TF binding region
BNIP2	TF binding region
ENSG00000140307	Chromatin interaction
ENSG00000140299	Chromatin interaction
ENSG00000259238	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1002181	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10152209	0.86[EUR][1000 genomes]
rs10152414	0.85[EUR][1000 genomes]
rs10152415	0.85[EUR][1000 genomes]
rs10162629	0.89[EUR][1000 genomes]
rs1046053	0.88[EUR][1000 genomes]
rs1057059	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11071465	0.86[EUR][1000 genomes]
rs11071468	0.89[EUR][1000 genomes]
rs11071469	0.89[EUR][1000 genomes]
rs1135148	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11634067	0.84[EUR][1000 genomes]
rs11853610	0.83[EUR][1000 genomes]
rs11854063	0.86[EUR][1000 genomes]
rs12438078	0.95[JPT][hapmap]
rs12441240	0.86[EUR][1000 genomes]
rs12593480	0.89[EUR][1000 genomes]
rs12708458	0.84[EUR][1000 genomes]
rs12708459	0.84[EUR][1000 genomes]
rs12902582	1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs12903647	0.84[EUR][1000 genomes]
rs12906392	0.84[EUR][1000 genomes]
rs12907554	0.88[EUR][1000 genomes]
rs12912652	0.80[EUR][1000 genomes]
rs1552031	0.91[EUR][1000 genomes]
rs1871500	0.86[EUR][1000 genomes]
rs1871503	0.81[EUR][1000 genomes]
rs2306355	0.87[EUR][1000 genomes]
rs2307272	0.90[EUR][1000 genomes]
rs2307275	0.91[EUR][1000 genomes]
rs28671744	0.84[EUR][1000 genomes]
rs2899649	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs34797071	0.84[EUR][1000 genomes]
rs34894301	0.82[EUR][1000 genomes]
rs3825870	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs4533213	0.92[EUR][1000 genomes]
rs4774340	0.85[EUR][1000 genomes]
rs4774341	0.86[EUR][1000 genomes]
rs4775191	0.81[EUR][1000 genomes]
rs4775195	0.88[EUR][1000 genomes]
rs4775197	0.87[EUR][1000 genomes]
rs6151458	0.92[EUR][1000 genomes]
rs6151459	0.85[EUR][1000 genomes]
rs6151460	0.92[EUR][1000 genomes]
rs6151461	0.92[EUR][1000 genomes]
rs6151462	0.92[EUR][1000 genomes]
rs6151467	0.92[EUR][1000 genomes]
rs6151470	0.92[EUR][1000 genomes]
rs6151472	0.90[EUR][1000 genomes]
rs6151474	0.92[EUR][1000 genomes]
rs6151477	0.92[EUR][1000 genomes]
rs6151483	0.82[EUR][1000 genomes]
rs6151486	0.92[EUR][1000 genomes]
rs6151487	0.82[EUR][1000 genomes]
rs6151501	0.88[EUR][1000 genomes]
rs6151503	0.91[EUR][1000 genomes]
rs6151504	0.91[EUR][1000 genomes]
rs6151506	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6151510	0.82[CEU][hapmap]
rs6151514	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6151525	0.81[EUR][1000 genomes]
rs6151528	0.89[EUR][1000 genomes]
rs6151529	0.89[EUR][1000 genomes]
rs6151532	0.89[EUR][1000 genomes]
rs6151533	0.90[EUR][1000 genomes]
rs6151535	0.81[CEU][hapmap];0.89[EUR][1000 genomes]
rs6151536	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs6151542	0.89[EUR][1000 genomes]
rs6151545	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6151551	0.80[EUR][1000 genomes]
rs6151553	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs6151568	0.87[EUR][1000 genomes]
rs6151571	0.87[EUR][1000 genomes]
rs6151574	0.87[EUR][1000 genomes]
rs6151580	0.85[EUR][1000 genomes]
rs6151581	0.84[EUR][1000 genomes]
rs6151586	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6151588	0.87[EUR][1000 genomes]
rs6151589	0.86[EUR][1000 genomes]
rs6151590	0.87[EUR][1000 genomes]
rs62015289	0.88[EUR][1000 genomes]
rs6494131	0.85[EUR][1000 genomes]
rs6494133	0.88[EUR][1000 genomes]
rs67820349	0.88[EUR][1000 genomes]
rs7162964	0.89[EUR][1000 genomes]
rs7164756	0.85[EUR][1000 genomes]
rs7180408	0.85[EUR][1000 genomes]
rs7182962	0.83[EUR][1000 genomes]
rs722163	0.92[EUR][1000 genomes]
rs722164	0.92[EUR][1000 genomes]
rs7497974	0.80[EUR][1000 genomes]
rs8033161	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8041394	1.00[YRI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3784389	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59949800-59980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:59950400-59979600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:59962000-59979400	Weak transcription	Fetal Heart	heart
4	chr15:59965000-59980200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:59968200-59979600	Weak transcription	Fetal Brain Male	brain
6	chr15:59969600-59980000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:59970600-59979800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:59970800-59979800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:59973200-59979600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr15:59973400-59980000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:59973600-59980000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:59973600-59980000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:59973600-59980000	Weak transcription	Esophagus	oesophagus
14	chr15:59973800-59979600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:59973800-59979600	Weak transcription	Brain Angular Gyrus	brain
16	chr15:59974000-59979600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:59974000-59979800	Weak transcription	Fetal Brain Female	brain
18	chr15:59974400-59979600	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:59974400-59979600	Weak transcription	Ovary	ovary
20	chr15:59974400-59979600	Weak transcription	Spleen	Spleen
21	chr15:59974400-59980000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:59974400-59980000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:59974400-59980000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:59974400-59980000	Weak transcription	Lung	lung
25	chr15:59974600-59979800	Weak transcription	Fetal Stomach	stomach
26	chr15:59974600-59980000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:59974800-59979600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr15:59974800-59979800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:59974800-59979800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:59975000-59979800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:59975200-59979600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:59976000-59979200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr15:59976200-59979800	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr15:59976400-59980400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:59976600-59979400	Genic enhancers	A549	lung
36	chr15:59976600-59979600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:59976600-59979800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr15:59976600-59979800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr15:59976600-59979800	Enhancers	NHDF-Ad	bronchial
40	chr15:59977000-59980400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr15:59977200-59979000	Enhancers	Colon Smooth Muscle	Colon
42	chr15:59977200-59979600	Enhancers	Adipose Nuclei	Adipose
43	chr15:59977200-59981000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:59977400-59979200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:59977400-59979200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:59977400-59979600	Enhancers	Duodenum Mucosa	Duodenum
47	chr15:59977400-59979800	Enhancers	Left Ventricle	heart
48	chr15:59977400-59980000	Enhancers	Gastric	stomach
49	chr15:59977400-59980000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr15:59977600-59979000	Enhancers	Colonic Mucosa	Colon

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