Variant report

Variant	rs9883806
Chromosome Location	chr3:111577836-111577837
allele	A/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	CHD2	chr3:111577489-111579719	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:111577360-111579652	HCT-116	colon:	n/a	n/a
3	CEBPB	chr3:111577759-111578268	A549	lung:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
4	POLR2A	chr3:111577188-111584197	MCF10A-Er-Src	breast:	n/a	n/a
5	RAD21	chr3:111577736-111578305	A549	lung:	n/a	n/a
6	ZNF143	chr3:111577557-111578242	Hela-S3	cervix:	n/a	n/a
7	SIN3AK20	chr3:111577816-111578142	A549	lung:	n/a	n/a
8	E2F1	chr3:111577579-111578872	Hela-S3	cervix:	n/a	chr3:111578683-111578693
9	USF2	chr3:111577507-111578355	Hela-S3	cervix:	n/a	chr3:111577993-111578004
10	MAFK	chr3:111577500-111579854	Hela-S3	cervix:	n/a	n/a
11	TBP	chr3:111577495-111578291	Hela-S3	cervix:	n/a	n/a
12	MYC	chr3:111577418-111578670	MCF10A-Er-Src	breast:	n/a	chr3:111578651-111578661
13	EP300	chr3:111577426-111578222	Hela-S3	cervix:	n/a	chr3:111577922-111577936
14	POLR2A	chr3:111577494-111580766	Hela-S3	cervix:	n/a	n/a
15	SIN3AK20	chr3:111577497-111579715	HCT-116	colon:	n/a	n/a
16	EP300	chr3:111577782-111579719	SK-N-SH	brain:	n/a	chr3:111578477-111578490 chr3:111578300-111578316 chr3:111578900-111578913 chr3:111577922-111577936 chr3:111578681-111578690
17	FOS	chr3:111577773-111578183	MCF10A-Er-Src	breast:	n/a	n/a
18	SMARCB1	chr3:111577559-111579652	Hela-S3	cervix:	n/a	n/a
19	CEBPB	chr3:111577822-111578569	HepG2	liver:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
20	FOXA1	chr3:111577830-111578423	HepG2	liver:	n/a	n/a
21	HA-E2F1	chr3:111577774-111579780	MCF-7	breast:	n/a	chr3:111578683-111578693 chr3:111579168-111579175 chr3:111579580-111579590
22	CEBPB	chr3:111577674-111578352	MCF-7	breast:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
23	STAT3	chr3:111577452-111578156	Hela-S3	cervix:	n/a	n/a
24	TFAP2A	chr3:111577378-111578577	Hela-S3	cervix:	n/a	chr3:111577962-111577977 chr3:111577963-111577974 chr3:111577965-111577973 chr3:111577964-111577972 chr3:111578326-111578334 chr3:111577963-111577974 chr3:111577964-111577972 chr3:111577963-111577974 chr3:111577965-111577973 chr3:111577965-111577973 chr3:111577963-111577974 chr3:111577964-111577972
25	POLR2A	chr3:111577424-111580051	Hela-S3	cervix:	n/a	n/a
26	NR3C1	chr3:111577819-111578129	A549	lung:	n/a	n/a
27	E2F4	chr3:111577521-111578212	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr3:111577624-111580773	HUVEC	blood vessel:	n/a	n/a
29	CEBPB	chr3:111577401-111578727	Hela-S3	cervix:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
30	MXI1	chr3:111577557-111578739	HepG2	liver:	n/a	n/a
31	FOXA1	chr3:111577817-111578047	T-47D	breast:	n/a	n/a
32	ZKSCAN1	chr3:111577455-111580075	Hela-S3	cervix:	n/a	n/a
33	MAX	chr3:111577383-111579825	A549	lung:	n/a	chr3:111578651-111578661
34	MAX	chr3:111577614-111578279	A549	lung:	n/a	n/a
35	RFX5	chr3:111577440-111578545	Hela-S3	cervix:	n/a	n/a
36	SMC3	chr3:111577452-111579872	Hela-S3	cervix:	n/a	chr3:111579404-111579412
37	STAT3	chr3:111577552-111578230	MCF10A-Er-Src	breast:	n/a	n/a
38	EP300	chr3:111577685-111578707	A549	lung:	n/a	chr3:111578477-111578490 chr3:111578300-111578316 chr3:111577922-111577936 chr3:111578681-111578690
39	CEBPB	chr3:111577744-111578264	A549	lung:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
40	FOS	chr3:111577812-111578177	MCF10A-Er-Src	breast:	n/a	n/a
41	MAX	chr3:111577480-111578754	A549	lung:	n/a	chr3:111578651-111578661
42	SIN3AK20	chr3:111577766-111578276	A549	lung:	n/a	n/a
43	CEBPB	chr3:111577815-111578205	HepG2	liver:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
44	GTF2F1	chr3:111577462-111578311	Hela-S3	cervix:	n/a	n/a
45	CHD1	chr3:111577445-111580853	IMR90	lung:	n/a	n/a
46	NR3C1	chr3:111577784-111578206	A549	lung:	n/a	n/a
47	TCF7L2	chr3:111577488-111578641	Hela-S3	cervix:	n/a	n/a
48	MAZ	chr3:111577734-111579691	Hela-S3	cervix:	n/a	chr3:111578651-111578661
49	FOXA2	chr3:111577813-111578511	A549	lung:	n/a	n/a
50	BRCA1	chr3:111577471-111578452	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111576494..111579081-chr3:111696421..111699159,2	MCF-7	breast:

Variant related genes	Relation type
PHLDB2	TF binding region
ENSG00000144827	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10212121	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10804493	0.84[EUR][1000 genomes]
rs10934114	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs11711475	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs12490718	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs12695246	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs1282931	0.96[CEU][hapmap];0.80[JPT][hapmap];0.92[EUR][1000 genomes]
rs1282932	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1282970	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs13063024	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063198	0.93[AFR][1000 genomes]
rs13063315	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083516	0.94[EUR][1000 genomes]
rs13101043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1913493	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1913494	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1913495	0.80[JPT][hapmap]
rs3925080	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs3925081	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs4381907	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs4383483	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs4583615	0.93[EUR][1000 genomes]
rs7626131	0.93[EUR][1000 genomes]
rs7637689	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs7638138	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs937553	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs937554	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs967011	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9827362	0.85[EUR][1000 genomes]
rs9846313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9883806	PHLDB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111577400-111578000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:111577400-111578000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:111577400-111578000	Flanking Active TSS	HUVEC	blood vessel
4	chr3:111577400-111578000	Flanking Active TSS	NH-A	brain
5	chr3:111577400-111578000	Flanking Active TSS	NHLF	lung
6	chr3:111577400-111578200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr3:111577400-111578200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:111577400-111578200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr3:111577400-111578200	Enhancers	Spleen	Spleen
10	chr3:111577400-111579200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
11	chr3:111577400-111580200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:111577400-111581000	Active TSS	Right Ventricle	heart
13	chr3:111577400-111581200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:111577400-111582000	Active TSS	Aorta	Aorta
15	chr3:111577400-111582000	Active TSS	HSMMtube	muscle
16	chr3:111577600-111578000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr3:111577600-111578000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr3:111577600-111578000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr3:111577600-111578000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:111577600-111578000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:111577600-111578000	Enhancers	Gastric	stomach
22	chr3:111577600-111578000	Enhancers	Small Intestine	intestine
23	chr3:111577600-111578000	Bivalent Enhancer	Dnd41	blood
24	chr3:111577600-111578000	Flanking Active TSS	HSMM	muscle
25	chr3:111577600-111578200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:111577600-111578200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
27	chr3:111577600-111578200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr3:111577600-111578200	Flanking Active TSS	Fetal Muscle Trunk	muscle
29	chr3:111577600-111578200	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr3:111577600-111578200	Flanking Active TSS	Fetal Stomach	stomach
31	chr3:111577600-111578400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:111577600-111578400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
33	chr3:111577600-111578600	Flanking Active TSS	Liver	Liver
34	chr3:111577600-111578800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
35	chr3:111577600-111579400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
36	chr3:111577600-111579600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:111577600-111579600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:111577600-111579600	Active TSS	Duodenum Mucosa	Duodenum
39	chr3:111577600-111580200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:111577600-111580200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
41	chr3:111577600-111580200	Active TSS	Placenta Amnion	Placenta Amnion
42	chr3:111577600-111580400	Active TSS	Fetal Heart	heart
43	chr3:111577600-111581200	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr3:111577600-111581800	Active TSS	Left Ventricle	heart
45	chr3:111577800-111578000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
46	chr3:111577800-111578000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr3:111577800-111578000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
48	chr3:111577800-111578000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:111577800-111578000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:111577800-111578000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain

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