Variant report

Variant	rs59383241
Chromosome Location	chr4:99576022-99576023
allele	A/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	SP1	chr4:99574838-99576212	HCT-116	colon:	n/a	chr4:99575619-99575633
2	JUND	chr4:99574951-99576208	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr4:99574890-99576086	SK-N-SH	brain:	n/a	n/a
4	FOS	chr4:99573969-99576098	MCF10A-Er-Src	breast:	n/a	chr4:99574466-99574475
5	POLR2A	chr4:99575483-99576089	PANC-1	pancreas:	n/a	n/a
6	TCF12	chr4:99574827-99576191	SK-N-SH	brain:	n/a	n/a
7	EP300	chr4:99574963-99576187	SK-N-SH	brain:	n/a	chr4:99575793-99575803
8	JUND	chr4:99574901-99576209	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr4:99575753-99576182	MCF10A-Er-Src	breast:	n/a	n/a
10	PBX3	chr4:99574941-99576028	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr4:99575404-99576097	A549	lung:	n/a	n/a
12	SIN3AK20	chr4:99575531-99576105	HCT-116	colon:	n/a	n/a
13	FOSL2	chr4:99574879-99576187	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr4:99575479-99576038	HUVEC	blood vessel:	n/a	n/a
15	CEBPB	chr4:99574855-99576128	HCT-116	colon:	n/a	n/a
16	TCF12	chr4:99574865-99576118	SK-N-SH	brain:	n/a	n/a
17	FOSL1	chr4:99574990-99576045	HCT-116	colon:	n/a	n/a
18	MAX	chr4:99574877-99576029	HCT-116	colon:	n/a	n/a
19	POLR2A	chr4:99575160-99576246	MCF10A-Er-Src	breast:	n/a	n/a
20	NFIC	chr4:99574880-99576104	SK-N-SH	brain:	n/a	n/a
21	ELF1	chr4:99574984-99576037	SK-N-SH	brain:	n/a	n/a
22	MYC	chr4:99574960-99576090	MCF10A-Er-Src	breast:	n/a	n/a
23	EP300	chr4:99574893-99576120	SK-N-SH	brain:	n/a	chr4:99575793-99575803
24	MXI1	chr4:99574840-99576168	IMR90	lung:	n/a	n/a
25	POLR2A	chr4:99574969-99576050	SK-N-SH	brain:	n/a	n/a
26	TEAD4	chr4:99574910-99576101	SK-N-SH	brain:	n/a	n/a
27	JUND	chr4:99574899-99576203	HCT-116	colon:	n/a	n/a
28	FOSL2	chr4:99575485-99576087	A549	lung:	n/a	n/a
29	STAT3	chr4:99574932-99576096	MCF10A-Er-Src	breast:	n/a	chr4:99575291-99575302 chr4:99575617-99575629
30	FOS	chr4:99573983-99576108	MCF10A-Er-Src	breast:	n/a	chr4:99574466-99574475
31	FOS	chr4:99575112-99576036	MCF10A-Er-Src	breast:	n/a	n/a
32	CBX3	chr4:99574896-99576044	HCT-116	colon:	n/a	chr4:99575721-99575732
33	MAX	chr4:99574834-99576028	HCT-116	colon:	n/a	n/a
34	GATA3	chr4:99574837-99576211	SK-N-SH	brain:	n/a	n/a
35	SP1	chr4:99574867-99576115	HCT-116	colon:	n/a	chr4:99575619-99575633
36	POLR2A	chr4:99575600-99576067	U87	brain:	n/a	n/a
37	POLR2A	chr4:99574923-99576081	HUVEC	blood vessel:	n/a	n/a
38	FOS	chr4:99575576-99576090	MCF10A-Er-Src	breast:	n/a	n/a
39	PBX3	chr4:99574891-99576027	SK-N-SH	brain:	n/a	n/a
40	FOS	chr4:99575030-99576080	HUVEC	blood vessel:	n/a	n/a
41	NFIC	chr4:99575661-99576099	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr4:99574971-99576113	IMR90	lung:	n/a	n/a
43	STAT3	chr4:99575046-99576085	MCF10A-Er-Src	breast:	n/a	chr4:99575291-99575302 chr4:99575617-99575629
44	POLR2A	chr4:99575600-99576082	U87	brain:	n/a	n/a
45	FOSL1	chr4:99574852-99576206	HCT-116	colon:	n/a	n/a
46	TEAD4	chr4:99574960-99576050	SK-N-SH	brain:	n/a	n/a
47	STAT3	chr4:99574964-99576111	MCF10A-Er-Src	breast:	n/a	chr4:99575291-99575302 chr4:99575617-99575629
48	FOSL2	chr4:99575540-99576047	SK-N-SH	brain:	n/a	n/a
49	JUND	chr4:99574955-99576070	HCT-116	colon:	n/a	n/a
50	MEF2A	chr4:99574916-99576057	SK-N-SH	brain:	n/a	chr4:99575951-99575959

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99575715..99578300-chr4:99579443..99581307,2	K562	blood:

Variant related genes	Relation type
ENSG00000260641	TF binding region
ENSG00000260641	Chromatin interaction
ENSG00000168785	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs28574900	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28722480	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28732372	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6532756	0.82[EUR][1000 genomes]
rs9991354	0.83[AMR][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	nsv966532	chr4:99571460-99581225	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59383241	RP11-1299A16.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99548000-99577000	Weak transcription	Esophagus	oesophagus
2	chr4:99569600-99578200	Weak transcription	Aorta	Aorta
3	chr4:99569600-99578400	Weak transcription	Spleen	Spleen
4	chr4:99570000-99576800	Weak transcription	Fetal Stomach	stomach
5	chr4:99570200-99577000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:99570200-99577000	Weak transcription	Fetal Heart	heart
7	chr4:99572600-99578000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:99573600-99576800	Enhancers	Brain Anterior Caudate	brain
9	chr4:99573800-99576600	Enhancers	Fetal Brain Male	brain
10	chr4:99573800-99576800	Enhancers	HMEC	breast
11	chr4:99573800-99577200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:99574000-99576400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:99574000-99577000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:99574200-99576600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr4:99574400-99576600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr4:99574400-99576600	Enhancers	Brain Germinal Matrix	brain
17	chr4:99574600-99577600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:99574800-99576800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:99575000-99576200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:99575000-99576400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:99575000-99576400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:99575200-99576600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr4:99575200-99576600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:99575200-99576800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr4:99575400-99576200	Weak transcription	Hela-S3	cervix
26	chr4:99575400-99576600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr4:99575400-99576600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr4:99575400-99576800	Weak transcription	Thymus	Thymus
29	chr4:99575400-99577000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:99575400-99577000	Enhancers	Brain Hippocampus Middle	brain
31	chr4:99575400-99577000	Weak transcription	Fetal Thymus	thymus
32	chr4:99575400-99577200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:99575400-99577200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:99575400-99577600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:99575400-99577800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:99575400-99578200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:99575400-99578200	Weak transcription	Left Ventricle	heart
38	chr4:99575600-99576200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:99575600-99576200	Enhancers	NHDF-Ad	bronchial
40	chr4:99575600-99576600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:99575600-99576600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr4:99575600-99576600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr4:99575600-99576600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:99575600-99576600	Weak transcription	Brain Angular Gyrus	brain
45	chr4:99575600-99576600	Enhancers	Brain Cingulate Gyrus	brain
46	chr4:99575600-99576600	Active TSS	Fetal Brain Female	brain
47	chr4:99575600-99576800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:99575600-99577000	Weak transcription	Fetal Muscle Leg	muscle
49	chr4:99575600-99577000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr4:99575600-99577600	Weak transcription	Colon Smooth Muscle	Colon

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