Variant report

Variant	rs2777744
Chromosome Location	chr9:33473893-33473894
allele	A/C
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	NRF1	chr9:33473677-33474320	GM12878	blood:	n/a	n/a
2	USF1	chr9:33473621-33474208	ECC-1	luminal epithelium:	n/a	n/a
3	SIN3AK20	chr9:33473687-33474161	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr9:33473596-33474345	Hela-S3	cervix:	n/a	n/a
5	SIN3AK20	chr9:33473630-33474312	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr9:33473190-33474398	GM12892	blood:	n/a	n/a
7	POLR2A	chr9:33473564-33473950	GM12878	blood:	n/a	n/a
8	POLR2A	chr9:33473626-33474392	HCT-116	colon:	n/a	n/a
9	ELK4	chr9:33473738-33474155	HEK293	kidney:	n/a	n/a
10	SRF	chr9:33473832-33474214	GM12878	blood:	n/a	n/a
11	RFX5	chr9:33473873-33474302	GM12878	blood:	n/a	n/a
12	USF1	chr9:33473677-33474142	H1-hESC	embryonic stem cell:	n/a	n/a
13	ATF3	chr9:33473839-33474316	A549	lung:	n/a	n/a
14	MXI1	chr9:33473491-33474341	HepG2	liver:	n/a	chr9:33473903-33473912
15	REST	chr9:33473713-33474302	HepG2	liver:	n/a	n/a
16	FOS	chr9:33473855-33474198	MCF10A-Er-Src	breast:	n/a	chr9:33474136-33474145
17	MYC	chr9:33473724-33474311	H1-hESC	embryonic stem cell:	n/a	chr9:33473904-33473913 chr9:33473902-33473912
18	SPI1	chr9:33473733-33474433	HL-60	blood:	n/a	n/a
19	ELF1	chr9:33473225-33474237	GM12878	blood:	n/a	n/a
20	POLR2A	chr9:33473618-33474296	Hela-S3	cervix:	n/a	n/a
21	ELF1	chr9:33473678-33474325	HepG2	liver:	n/a	n/a
22	SP1	chr9:33473532-33474375	HCT-116	colon:	n/a	chr9:33474043-33474052 chr9:33473906-33473917 chr9:33473999-33474020
23	POLR2A	chr9:33473551-33474421	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr9:33473620-33473936	GM12878	blood:	n/a	n/a
25	YY1	chr9:33473499-33474212	GM12892	blood:	n/a	n/a
26	MAX	chr9:33473411-33474358	ECC-1	luminal epithelium:	n/a	chr9:33473904-33473913 chr9:33473902-33473912
27	FOXA1	chr9:33473713-33474405	HepG2	liver:	n/a	n/a
28	MYC	chr9:33473629-33474184	MCF-7	breast:	n/a	chr9:33473904-33473913 chr9:33473902-33473912
29	POLR2A	chr9:33473619-33474319	GM12892	blood:	n/a	n/a
30	KAP1	chr9:33473788-33474246	U2OS	brain:	n/a	n/a
31	USF1	chr9:33473691-33474136	A549	lung:	n/a	n/a
32	EP300	chr9:33473828-33474358	A549	lung:	n/a	chr9:33474126-33474140
33	POLR2A	chr9:33473639-33474210	Gliobla	brain:	n/a	n/a
34	MAX	chr9:33473535-33474391	K562	blood:	n/a	chr9:33473904-33473913 chr9:33473902-33473912
35	MAX	chr9:33473363-33474447	MCF-7	breast:	n/a	chr9:33473904-33473913 chr9:33473902-33473912
36	CREB1	chr9:33473577-33474360	GM12878	blood:	n/a	n/a
37	EGR1	chr9:33473780-33474142	K562	blood:	n/a	chr9:33473905-33473914 chr9:33473903-33473917 chr9:33473904-33473914 chr9:33473904-33473914
38	POLR2A	chr9:33473597-33474373	IMR90	lung:	n/a	n/a
39	ATF2	chr9:33473760-33474250	H1-hESC	embryonic stem cell:	n/a	n/a
40	CEBPB	chr9:33473686-33474278	IMR90	lung:	n/a	n/a
41	CREB1	chr9:33473795-33474313	ECC-1	luminal epithelium:	n/a	n/a
42	MYC	chr9:33473671-33474201	MCF-7	breast:	n/a	chr9:33473904-33473913 chr9:33473902-33473912
43	POLR2A	chr9:33473652-33473959	HepG2	liver:	n/a	n/a
44	ZNF143	chr9:33473770-33474145	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr9:33473585-33474394	HepG2	liver:	n/a	n/a
46	ATF1	chr9:33473831-33474242	K562	blood:	n/a	n/a
47	MAX	chr9:33473477-33474365	H1-hESC	embryonic stem cell:	n/a	chr9:33473904-33473913 chr9:33473902-33473912
48	EBF1	chr9:33473807-33474291	GM12878	blood:	n/a	n/a
49	TAF1	chr9:33473680-33474304	MCF-7	breast:	n/a	n/a
50	MYC	chr9:33473615-33474311	MCF10A-Er-Src	breast:	n/a	chr9:33473904-33473913 chr9:33473902-33473912

No.	Distal block	Cell Line	Cell type
1	chr9:33290539..33292968-chr9:33470956..33474954,3	MCF-7	breast:
2	chr9:33259956..33261573-chr9:33472646..33474326,2	K562	blood:
3	chr9:33445821..33447609-chr9:33472349..33474000,2	MCF-7	breast:

Variant related genes	Relation type
NOL6	TF binding region
ENSG00000165272	Chromatin interaction
ENSG00000086102	Chromatin interaction
ENSG00000107262	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10758210	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10813990	0.96[CEU][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap]
rs10971543	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10971544	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11787590	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12002293	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12005354	0.84[CHD][hapmap];0.86[GIH][hapmap]
rs12005759	0.87[CHD][hapmap];0.86[GIH][hapmap];0.81[MKK][hapmap]
rs2777740	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2777741	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2777742	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2777753	0.88[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap]
rs2785205	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2785206	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2785210	0.94[ASW][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2989934	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989938	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2992817	0.82[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap]
rs2992822	0.83[EUR][1000 genomes]
rs2992824	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2992825	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2992826	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2992828	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2992829	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs521769	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs560833	0.94[ASW][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs583076	0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs61294221	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62546519	0.83[ASN][1000 genomes]
rs6476412	0.82[EUR][1000 genomes]
rs678859	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7023317	0.96[CEU][hapmap];0.83[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs7032025	0.80[EUR][1000 genomes]
rs7032925	0.80[EUR][1000 genomes]
rs7033908	0.80[EUR][1000 genomes]
rs7047660	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9696671	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024207	chr9:33296368-33574892	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv518168	chr9:33465182-33478434	Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2777744	AQP3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:33472400-33474000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr9:33472400-33475000	Active TSS	Fetal Brain Female	brain
3	chr9:33472600-33474600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:33472600-33474800	Active TSS	H1 Cell Line	embryonic stem cell
5	chr9:33472600-33474800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr9:33472600-33475000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:33472600-33475000	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr9:33472600-33475000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr9:33472600-33475000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr9:33472600-33475000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr9:33472600-33475000	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr9:33472600-33475000	Active TSS	Fetal Kidney	kidney
13	chr9:33472600-33475000	Active TSS	A549	lung
14	chr9:33472600-33475000	Active TSS	NHLF	lung
15	chr9:33472800-33474600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:33472800-33474600	Active TSS	Psoas Muscle	Psoas
17	chr9:33472800-33474800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:33472800-33474800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:33472800-33474800	Active TSS	Right Ventricle	heart
20	chr9:33472800-33474800	Active TSS	HSMM	muscle
21	chr9:33472800-33475000	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr9:33472800-33475000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:33472800-33475000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:33472800-33475000	Active TSS	GM12878-XiMat	blood
25	chr9:33472800-33475000	Active TSS	HMEC	breast
26	chr9:33472800-33475000	Active TSS	K562	blood
27	chr9:33472800-33475000	Active TSS	NH-A	brain
28	chr9:33473000-33474400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:33473000-33474400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr9:33473000-33474400	Bivalent/Poised TSS	HepG2	liver
31	chr9:33473000-33474600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:33473000-33474800	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr9:33473000-33474800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr9:33473000-33474800	Active TSS	Fetal Intestine Large	intestine
35	chr9:33473000-33474800	Active TSS	NHEK	skin
36	chr9:33473000-33475000	Active TSS	Muscle Satellite Cultured Cells	--
37	chr9:33473000-33475000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:33473000-33475000	Active TSS	NHDF-Ad	bronchial
39	chr9:33473200-33474400	Active TSS	Stomach Mucosa	stomach
40	chr9:33473200-33474600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr9:33473200-33474600	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr9:33473200-33474600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:33473200-33474600	Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr9:33473200-33474600	Active TSS	Fetal Intestine Small	intestine
45	chr9:33473200-33474600	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr9:33473200-33474800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr9:33473200-33474800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:33473200-33474800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr9:33473200-33474800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr9:33473200-33474800	Active TSS	Pancreatic Islets	Pancreatic Islet

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