Variant report

Variant	rs17016047
Chromosome Location	chr4:143329121-143329122
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	MAX	chr4:143328992-143329640	A549	lung:	n/a	chr4:143329212-143329221 chr4:143329213-143329222
2	CHD2	chr4:143328801-143329781	Hela-S3	cervix:	n/a	n/a
3	EP300	chr4:143328928-143329772	SK-N-SH	brain:	n/a	chr4:143329212-143329221 chr4:143329213-143329222 chr4:143329415-143329429
4	CEBPB	chr4:143328758-143329568	ECC-1	luminal epithelium:	n/a	n/a
5	STAT3	chr4:143328547-143329620	MCF10A-Er-Src	breast:	n/a	chr4:143328569-143328589 chr4:143328572-143328586 chr4:143328575-143328583 chr4:143329212-143329221 chr4:143329213-143329222
6	EP300	chr4:143329055-143329358	SK-N-SH_RA	brain:	n/a	chr4:143329212-143329221 chr4:143329213-143329222
7	CEBPB	chr4:143328675-143329756	A549	lung:	n/a	n/a
8	SP1	chr4:143328783-143329834	A549	lung:	n/a	n/a
9	FOSL2	chr4:143328720-143329729	A549	lung:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
10	CEBPB	chr4:143328829-143329661	A549	lung:	n/a	n/a
11	EP300	chr4:143328866-143329802	A549	lung:	n/a	chr4:143329212-143329221 chr4:143329213-143329222 chr4:143329415-143329429
12	EP300	chr4:143328688-143329847	A549	lung:	n/a	chr4:143329212-143329221 chr4:143329213-143329222 chr4:143329415-143329429
13	NFIC	chr4:143328977-143329579	SK-N-SH	brain:	n/a	n/a
14	FOS	chr4:143328862-143329510	MCF10A-Er-Src	breast:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
15	STAT3	chr4:143328413-143329597	MCF10A-Er-Src	breast:	n/a	chr4:143328569-143328589 chr4:143328572-143328586 chr4:143328575-143328583 chr4:143329212-143329221 chr4:143329213-143329222
16	FOS	chr4:143328935-143329541	HUVEC	blood vessel:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
17	FOS	chr4:143328823-143330281	MCF10A-Er-Src	breast:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221 chr4:143330185-143330197
18	JUND	chr4:143329079-143329609	SK-N-SH	brain:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
19	JUN	chr4:143329081-143329493	HUVEC	blood vessel:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
20	EP300	chr4:143328796-143329505	Hela-S3	cervix:	n/a	chr4:143329212-143329221 chr4:143329213-143329222 chr4:143329415-143329429
21	TEAD4	chr4:143328966-143329826	A549	lung:	n/a	n/a
22	STAT3	chr4:143329060-143329636	MCF10A-Er-Src	breast:	n/a	chr4:143329212-143329221 chr4:143329213-143329222
23	CEBPB	chr4:143328577-143329755	HCT-116	colon:	n/a	n/a
24	FOSL1	chr4:143328684-143329731	HCT-116	colon:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
25	EP300	chr4:143329103-143329773	ECC-1	luminal epithelium:	n/a	chr4:143329212-143329221 chr4:143329213-143329222 chr4:143329415-143329429
26	SP1	chr4:143328599-143329784	HCT-116	colon:	n/a	n/a
27	MEF2A	chr4:143328906-143329557	SK-N-SH	brain:	n/a	n/a
28	FOSL2	chr4:143329005-143329579	A549	lung:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
29	TEAD4	chr4:143329062-143329593	SK-N-SH	brain:	n/a	n/a
30	CEBPB	chr4:143328825-143329652	A549	lung:	n/a	n/a
31	USF1	chr4:143329083-143329519	A549	lung:	n/a	n/a
32	JUND	chr4:143328643-143329586	HCT-116	colon:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
33	ESR1	chr4:143329044-143329864	ECC-1	luminal epithelium:	n/a	chr4:143329474-143329489
34	TCF12	chr4:143329060-143329557	A549	lung:	n/a	n/a
35	ATF3	chr4:143328695-143329751	HCT-116	colon:	n/a	n/a
36	NR3C1	chr4:143329077-143329728	A549	lung:	n/a	n/a
37	JUND	chr4:143328677-143329667	HCT-116	colon:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
38	TCF12	chr4:143328967-143329766	SK-N-SH	brain:	n/a	n/a
39	GATA2	chr4:143328862-143329625	HUVEC	blood vessel:	n/a	chr4:143329140-143329149
40	GABPA	chr4:143328945-143329584	A549	lung:	n/a	n/a
41	TEAD4	chr4:143329075-143329765	ECC-1	luminal epithelium:	n/a	n/a
42	MYC	chr4:143328997-143329597	MCF10A-Er-Src	breast:	n/a	chr4:143329212-143329221 chr4:143329213-143329222
43	POLR2A	chr4:143328984-143329320	MCF10A-Er-Src	breast:	n/a	n/a
44	STAT3	chr4:143328821-143329574	MCF10A-Er-Src	breast:	n/a	chr4:143329212-143329221 chr4:143329213-143329222
45	POLR2A	chr4:143328803-143329506	MCF10A-Er-Src	breast:	n/a	n/a
46	FOSL2	chr4:143329060-143329549	SK-N-SH	brain:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
47	EP300	chr4:143328862-143329884	ECC-1	luminal epithelium:	n/a	chr4:143329212-143329221 chr4:143329213-143329222 chr4:143329415-143329429
48	FOSL2	chr4:143329087-143329452	MCF-7	breast:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221
49	REST	chr4:143328911-143329568	A549	lung:	n/a	n/a
50	JUND	chr4:143328794-143329690	Hela-S3	cervix:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221

No.	Distal block	Cell Line	Cell type
1	chr4:143327592..143330271-chr4:143378912..143381553,2	MCF-7	breast:
2	chr4:143327221..143331819-chr4:143394116..143397905,6	MCF-7	breast:
3	chr4:143327412..143330052-chr4:143383937..143385936,2	MCF-7	breast:
4	chr4:143327600..143329351-chr4:143391019..143392587,2	MCF-7	breast:
5	chr4:143326852..143329330-chr4:143520781..143523143,2	MCF-7	breast:
6	chr4:143323626..143325827-chr4:143327783..143329444,2	MCF-7	breast:
7	chr4:143326578..143329374-chr4:143334403..143336752,2	MCF-7	breast:

Variant related genes	Relation type
INPP4B	TF binding region
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10519654	1.00[AMR][1000 genomes]
rs10519658	0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1489579	1.00[AMR][1000 genomes]
rs16998546	1.00[AMR][1000 genomes]
rs17016073	0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs17016097	0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28361347	1.00[AMR][1000 genomes]
rs28552507	1.00[AMR][1000 genomes]
rs55734648	1.00[AMR][1000 genomes]
rs55924247	1.00[AMR][1000 genomes]
rs58466279	1.00[AMR][1000 genomes]
rs59339281	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60408738	1.00[AMR][1000 genomes]
rs61368063	1.00[AMR][1000 genomes]
rs61643803	1.00[AMR][1000 genomes]
rs6845221	1.00[AMR][1000 genomes]
rs72941201	1.00[AMR][1000 genomes]
rs72944962	1.00[AMR][1000 genomes]
rs72944976	1.00[AMR][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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv968011	chr4:143325315-143333139	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143326400-143330400	Enhancers	Hela-S3	cervix
2	chr4:143327000-143330000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:143327000-143330000	Enhancers	HUVEC	blood vessel
4	chr4:143327000-143330400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:143327200-143329400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr4:143327200-143330000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:143327200-143330200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:143327200-143330200	Enhancers	NH-A	brain
9	chr4:143327400-143329200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:143327400-143329600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr4:143327400-143330000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:143327400-143330600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:143327600-143329200	Enhancers	NHLF	lung
14	chr4:143327600-143330400	Enhancers	HSMM	muscle
15	chr4:143327600-143331200	Enhancers	NHEK	skin
16	chr4:143327600-143335600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:143327800-143329400	Enhancers	Fetal Heart	heart
18	chr4:143327800-143330000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr4:143327800-143330000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:143327800-143330200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:143327800-143330600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:143327800-143335600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:143328000-143330000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:143328000-143330000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:143328000-143330000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:143328000-143330400	Enhancers	A549	lung
27	chr4:143328200-143329200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr4:143328200-143329200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:143328200-143329200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:143328200-143329400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:143328200-143329600	Enhancers	Dnd41	blood
32	chr4:143328200-143330000	Enhancers	Osteobl	bone
33	chr4:143328400-143331600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr4:143328400-143331600	Enhancers	HMEC	breast
35	chr4:143328600-143330400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr4:143328600-143330400	Enhancers	NHDF-Ad	bronchial
37	chr4:143328600-143330600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:143328600-143335200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:143328600-143336400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:143328800-143329600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:143328800-143329600	Enhancers	Psoas Muscle	Psoas
42	chr4:143328800-143329800	Weak transcription	Stomach Mucosa	stomach
43	chr4:143328800-143332600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:143328800-143334200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:143329000-143329600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:143329000-143329600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:143329000-143329800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:143329000-143329800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr4:143329000-143329800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr4:143329000-143330000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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