Variant report

Variant	rs13101043
Chromosome Location	chr3:111577787-111577788
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	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	E2F1	chr3:111577579-111578872	Hela-S3	cervix:	n/a	chr3:111578683-111578693
8	USF2	chr3:111577507-111578355	Hela-S3	cervix:	n/a	chr3:111577993-111578004
9	MAFK	chr3:111577500-111579854	Hela-S3	cervix:	n/a	n/a
10	TBP	chr3:111577495-111578291	Hela-S3	cervix:	n/a	n/a
11	MYC	chr3:111577418-111578670	MCF10A-Er-Src	breast:	n/a	chr3:111578651-111578661
12	EP300	chr3:111577426-111578222	Hela-S3	cervix:	n/a	chr3:111577922-111577936
13	POLR2A	chr3:111577494-111580766	Hela-S3	cervix:	n/a	n/a
14	SIN3AK20	chr3:111577497-111579715	HCT-116	colon:	n/a	n/a
15	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
16	FOS	chr3:111577773-111578183	MCF10A-Er-Src	breast:	n/a	n/a
17	SMARCB1	chr3:111577559-111579652	Hela-S3	cervix:	n/a	n/a
18	HA-E2F1	chr3:111577774-111579780	MCF-7	breast:	n/a	chr3:111578683-111578693 chr3:111579168-111579175 chr3:111579580-111579590
19	CEBPB	chr3:111577674-111578352	MCF-7	breast:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
20	STAT3	chr3:111577452-111578156	Hela-S3	cervix:	n/a	n/a
21	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
22	POLR2A	chr3:111577424-111580051	Hela-S3	cervix:	n/a	n/a
23	E2F4	chr3:111577521-111578212	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr3:111577624-111580773	HUVEC	blood vessel:	n/a	n/a
25	CEBPB	chr3:111577401-111578727	Hela-S3	cervix:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
26	MXI1	chr3:111577557-111578739	HepG2	liver:	n/a	n/a
27	ZKSCAN1	chr3:111577455-111580075	Hela-S3	cervix:	n/a	n/a
28	MAX	chr3:111577383-111579825	A549	lung:	n/a	chr3:111578651-111578661
29	MAX	chr3:111577614-111578279	A549	lung:	n/a	n/a
30	RFX5	chr3:111577440-111578545	Hela-S3	cervix:	n/a	n/a
31	SMC3	chr3:111577452-111579872	Hela-S3	cervix:	n/a	chr3:111579404-111579412
32	STAT3	chr3:111577552-111578230	MCF10A-Er-Src	breast:	n/a	n/a
33	EP300	chr3:111577685-111578707	A549	lung:	n/a	chr3:111578477-111578490 chr3:111578300-111578316 chr3:111577922-111577936 chr3:111578681-111578690
34	CEBPB	chr3:111577744-111578264	A549	lung:	n/a	chr3:111577924-111577935 chr3:111578002-111578019
35	MAX	chr3:111577480-111578754	A549	lung:	n/a	chr3:111578651-111578661
36	SIN3AK20	chr3:111577766-111578276	A549	lung:	n/a	n/a
37	GTF2F1	chr3:111577462-111578311	Hela-S3	cervix:	n/a	n/a
38	CHD1	chr3:111577445-111580853	IMR90	lung:	n/a	n/a
39	NR3C1	chr3:111577784-111578206	A549	lung:	n/a	n/a
40	TCF7L2	chr3:111577488-111578641	Hela-S3	cervix:	n/a	n/a
41	MAZ	chr3:111577734-111579691	Hela-S3	cervix:	n/a	chr3:111578651-111578661
42	BRCA1	chr3:111577471-111578452	Hela-S3	cervix:	n/a	n/a
43	RAD21	chr3:111577412-111578254	Hela-S3	cervix:	n/a	n/a
44	SP1	chr3:111577629-111578863	A549	lung:	n/a	chr3:111578651-111578661 chr3:111578547-111578561 chr3:111578551-111578560 chr3:111578652-111578661 chr3:111578210-111578224 chr3:111578651-111578660 chr3:111578650-111578662 chr3:111578445-111578459 chr3:111578650-111578662
45	RAD21	chr3:111577748-111579964	IMR90	lung:	n/a	chr3:111579591-111579603
46	MXI1	chr3:111577501-111578287	Hela-S3	cervix:	n/a	n/a
47	SMARCC1	chr3:111577422-111579914	Hela-S3	cervix:	n/a	n/a
48	JUND	chr3:111577299-111579719	SK-N-SH	brain:	n/a	chr3:111578782-111578796
49	POLR2A	chr3:111577394-111580154	Hela-S3	cervix:	n/a	n/a
50	EP300	chr3:111577579-111578681	A549	lung:	n/a	chr3:111578477-111578490 chr3:111578300-111578316 chr3:111577922-111577936

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:111577743-111577793	HCT-116	colon:	n/a
2	chr3:111577743-111577793	AG09319	gingival:	n/a
3	chr3:111577743-111577793	GM12878	blood:	n/a
4	chr3:111577743-111577793	U87	brain:	n/a
5	chr3:111577743-111577793	ProgFib	skin:	n/a
6	chr3:111577743-111577793	HRPEpiC	eye:	n/a
7	chr3:111577743-111577793	NHDF-neo	bronchial:	n/a
8	chr3:111577743-111577793	HCF	heart:	n/a
9	chr3:111577743-111577793	K562	blood:	n/a
10	chr3:111577743-111577793	NHBE	bronchial:	n/a
11	chr3:111577743-111577793	HAEpiC	amniotic membrane:	n/a
12	chr3:111577743-111577793	HepG2	liver:	n/a
13	chr3:111577743-111577793	Hela-S3	cervix:	n/a
14	chr3:111577743-111577793	T-47D	breast:	n/a
15	chr3:111577743-111577793	HRE	kidney:	n/a
16	chr3:111577743-111577793	A549	lung:	n/a
17	chr3:111577743-111577793	ovcar-3	ovarian:	n/a
18	chr3:111577743-111577793	NH-A	brain:	n/a
19	chr3:111577743-111577793	AG10803	skin:	n/a
20	chr3:111577743-111577793	SK-N-MC	brain:	n/a
21	chr3:111577743-111577793	BJ	skin:	n/a
22	chr3:111577743-111577793	HCM	heart:	n/a
23	chr3:111577743-111577793	MCF-7	breast:	n/a
24	chr3:111577743-111577793	LNCaP	prostate:	n/a
25	chr3:111577743-111577793	HPAEpiC	pulmonary alveolar:	n/a
26	chr3:111577743-111577793	GM12891	blood:	n/a
27	chr3:111577743-111577793	HUVEC	blood vessel:	n/a
28	chr3:111577743-111577793	RPTEC	kidney:	n/a
29	chr3:111577743-111577793	IMR90	lung:	fetal
30	chr3:111577743-111577793	HEK293	kidney:	embryo
31	chr3:111577743-111577793	H1-hESC	embryonic stem cell:	embryo
32	chr3:111577743-111577793	GM12892	blood:	n/a
33	chr3:111577743-111577793	HMEC	breast:	n/a
34	chr3:111577743-111577793	MCF10A-Er-Src	breast:	n/a
35	chr3:111577743-111577793	AG09309	skin:	n/a
36	chr3:111577743-111577793	BE2_C	brain:	n/a
37	chr3:111577743-111577793	HCPEpiC	choroid plexus:	n/a
38	chr3:111577743-111577793	HIPEpiC	eye:	n/a
39	chr3:111577743-111577793	HNPCEpiC	eye:	n/a
40	chr3:111577743-111577793	SKMC	muscle:	n/a
41	chr3:111577743-111577793	PFSK-1	brain:	n/a
42	chr3:111577743-111577793	CMK	blood:	n/a
43	chr3:111577743-111577793	GM06990	blood:	n/a
44	chr3:111577743-111577793	SK-N-SH	brain:	n/a
45	chr3:111577743-111577793	Caco-2	colon:	n/a
46	chr3:111577743-111577793	NB4	blood:	n/a
47	chr3:111577743-111577793	PANC-1	pancreas:	n/a
48	chr3:111577743-111577793	Hepatocyte	liver:	n/a
49	chr3:111577743-111577793	SK-N-SH_RA	brain:	n/a
50	chr3:111577743-111577793	GM19239	blood:	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
PHLDB2	CpG island
ENSG00000144827	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10212121	0.84[EUR][1000 genomes]
rs10804493	0.83[EUR][1000 genomes]
rs10934114	0.93[EUR][1000 genomes]
rs11711475	0.95[EUR][1000 genomes]
rs12490718	0.96[EUR][1000 genomes]
rs12695246	0.93[EUR][1000 genomes]
rs1282931	0.92[EUR][1000 genomes]
rs1282932	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1282970	0.94[EUR][1000 genomes]
rs13063024	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083516	0.93[EUR][1000 genomes]
rs1913493	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1913494	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3925080	0.92[EUR][1000 genomes]
rs3925081	0.92[EUR][1000 genomes]
rs4381907	0.92[EUR][1000 genomes]
rs4383483	0.92[EUR][1000 genomes]
rs4583615	0.92[EUR][1000 genomes]
rs7626131	0.92[EUR][1000 genomes]
rs7637689	0.92[EUR][1000 genomes]
rs7638138	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs937553	0.92[EUR][1000 genomes]
rs937554	0.93[EUR][1000 genomes]
rs967011	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9827362	0.84[EUR][1000 genomes]
rs9846313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883806	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
rs13101043	PHLDB2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111577400-111577800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:111577400-111577800	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
3	chr3:111577400-111577800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:111577400-111577800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
5	chr3:111577400-111577800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
6	chr3:111577400-111577800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
7	chr3:111577400-111577800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
8	chr3:111577400-111577800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
9	chr3:111577400-111577800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
10	chr3:111577400-111577800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:111577400-111577800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:111577400-111577800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr3:111577400-111577800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:111577400-111577800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr3:111577400-111577800	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
16	chr3:111577400-111577800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:111577400-111577800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:111577400-111577800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:111577400-111577800	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr3:111577400-111577800	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr3:111577400-111577800	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr3:111577400-111577800	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr3:111577400-111577800	Flanking Active TSS	A549	lung
24	chr3:111577400-111577800	Flanking Active TSS	Hela-S3	cervix
25	chr3:111577400-111577800	Flanking Active TSS	HepG2	liver
26	chr3:111577400-111577800	Flanking Active TSS	HMEC	breast
27	chr3:111577400-111577800	Flanking Active TSS	NHEK	skin
28	chr3:111577400-111577800	Flanking Active TSS	Osteobl	bone
29	chr3:111577400-111578000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:111577400-111578000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:111577400-111578000	Flanking Active TSS	HUVEC	blood vessel
32	chr3:111577400-111578000	Flanking Active TSS	NH-A	brain
33	chr3:111577400-111578000	Flanking Active TSS	NHLF	lung
34	chr3:111577400-111578200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
35	chr3:111577400-111578200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:111577400-111578200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr3:111577400-111578200	Enhancers	Spleen	Spleen
38	chr3:111577400-111579200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
39	chr3:111577400-111580200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:111577400-111581000	Active TSS	Right Ventricle	heart
41	chr3:111577400-111581200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:111577400-111582000	Active TSS	Aorta	Aorta
43	chr3:111577400-111582000	Active TSS	HSMMtube	muscle
44	chr3:111577600-111577800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:111577600-111577800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:111577600-111577800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:111577600-111577800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:111577600-111577800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:111577600-111577800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
50	chr3:111577600-111577800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

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