Variant report

Variant	rs59339281
Chromosome Location	chr4:143328313-143328314
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	POLR2A	chr4:143324039-143328578	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr4:143328085-143329757	MCF10A-Er-Src	breast:	n/a	chr4:143329213-143329221 chr4:143329213-143329222 chr4:143329214-143329221 chr4:143328294-143328303

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	chr4:143326731..143329100-chr4:143388048..143390704,2	MCF-7	breast:
7	chr4:143323626..143325827-chr4:143327783..143329444,2	MCF-7	breast:
8	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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10519658	1.00[AMR][1000 genomes]
rs1489579	1.00[AMR][1000 genomes]
rs16998546	1.00[AMR][1000 genomes]
rs17016047	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17016073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17016097	1.00[AMR][1000 genomes]
rs28361347	1.00[AMR][1000 genomes]
rs28552507	1.00[AMR][1000 genomes]
rs55734648	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55924247	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58466279	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60408738	1.00[AMR][1000 genomes]
rs61368063	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61643803	1.00[AMR][1000 genomes]
rs6845221	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72941201	1.00[AMR][1000 genomes]
rs72944962	1.00[AMR][1000 genomes]
rs72944976	0.97[AFR][1000 genomes];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:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143326400-143328600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr4:143326400-143329000	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr4:143326400-143330400	Enhancers	Hela-S3	cervix
4	chr4:143326600-143328400	Flanking Active TSS	HMEC	breast
5	chr4:143326600-143328600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:143326600-143328800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:143326600-143329000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr4:143326600-143329000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr4:143326600-143329000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr4:143326600-143329000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr4:143327000-143328400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:143327000-143328800	Enhancers	Stomach Mucosa	stomach
13	chr4:143327000-143329000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr4:143327000-143329000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr4:143327000-143329000	Enhancers	Fetal Intestine Small	intestine
16	chr4:143327000-143329000	Enhancers	Fetal Thymus	thymus
17	chr4:143327000-143329000	Enhancers	Thymus	Thymus
18	chr4:143327000-143330000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:143327000-143330000	Enhancers	HUVEC	blood vessel
20	chr4:143327000-143330400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:143327200-143329000	Enhancers	Primary hematopoietic stem cells	blood
22	chr4:143327200-143329000	Enhancers	Fetal Muscle Leg	muscle
23	chr4:143327200-143329000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr4:143327200-143329000	Enhancers	Small Intestine	intestine
25	chr4:143327200-143329400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr4:143327200-143330000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:143327200-143330200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:143327200-143330200	Enhancers	NH-A	brain
29	chr4:143327400-143328800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr4:143327400-143329000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr4:143327400-143329000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr4:143327400-143329200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr4:143327400-143329600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr4:143327400-143330000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:143327400-143330600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:143327600-143328400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:143327600-143328600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr4:143327600-143328600	Enhancers	Fetal Lung	lung
39	chr4:143327600-143328600	Weak transcription	Placenta	Placenta
40	chr4:143327600-143328800	Weak transcription	Psoas Muscle	Psoas
41	chr4:143327600-143328800	Weak transcription	Right Atrium	heart
42	chr4:143327600-143328800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:143327600-143329000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr4:143327600-143329000	Enhancers	HSMMtube	muscle
45	chr4:143327600-143329200	Enhancers	NHLF	lung
46	chr4:143327600-143330400	Enhancers	HSMM	muscle
47	chr4:143327600-143331200	Enhancers	NHEK	skin
48	chr4:143327600-143335600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:143327800-143328800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:143327800-143328800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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