Variant report

Variant	rs59055207
Chromosome Location	chr4:79559985-79559986
allele	A/C
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	RELA	chr4:79558885-79560367	GM18951	blood:	n/a	n/a
2	REST	chr4:79559928-79560122	Hela-S3	cervix:	n/a	n/a
3	NFIC	chr4:79559494-79560308	GM12878	blood:	n/a	n/a
4	MTA3	chr4:79559400-79560150	GM12878	blood:	n/a	n/a
5	EP300	chr4:79558934-79560251	GM12878	blood:	n/a	chr4:79560125-79560139 chr4:79560020-79560034
6	WRNIP1	chr4:79559773-79560310	GM12878	blood:	n/a	n/a
7	RELA	chr4:79558837-79560320	GM10847	blood:	n/a	n/a
8	SPI1	chr4:79559815-79560232	GM12891	blood:	n/a	chr4:79560020-79560029
9	CHD2	chr4:79559680-79560344	GM12878	blood:	n/a	n/a
10	RUNX3	chr4:79559482-79560233	GM12878	blood:	n/a	n/a
11	IRF1	chr4:79559978-79560144	K562	blood:	n/a	chr4:79560015-79560029 chr4:79560017-79560031 chr4:79560055-79560069 chr4:79560016-79560030
12	SP1	chr4:79559767-79560182	GM12878	blood:	n/a	n/a
13	STAT3	chr4:79559445-79560211	GM12878	blood:	n/a	chr4:79560018-79560029
14	STAT1	chr4:79559775-79560278	GM12878	blood:	n/a	chr4:79560018-79560029
15	ATF2	chr4:79559350-79560346	GM12878	blood:	n/a	n/a
16	ZNF384	chr4:79559493-79560251	GM12878	blood:	n/a	n/a
17	SPI1	chr4:79559920-79560123	GM12878	blood:	n/a	chr4:79560020-79560029
18	RUNX3	chr4:79559741-79560209	GM12878	blood:	n/a	n/a
19	CUX1	chr4:79559571-79560160	GM12878	blood:	n/a	n/a
20	IRF4	chr4:79559441-79560112	GM12878	blood:	n/a	n/a
21	ZNF384	chr4:79559852-79560113	K562	blood:	n/a	n/a
22	BATF	chr4:79559524-79560027	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr4:79559798-79560305	GM12878	blood:	n/a	n/a
24	SMC3	chr4:79559662-79560265	GM12878	blood:	n/a	n/a
25	SPI1	chr4:79559816-79560209	GM12878	blood:	n/a	chr4:79560020-79560029
26	BHLHE40	chr4:79559595-79560217	GM12878	blood:	n/a	n/a
27	EBF1	chr4:79559751-79560125	GM12878	blood:	n/a	n/a
28	EBF1	chr4:79559563-79560230	GM12878	blood:	n/a	n/a
29	SPI1	chr4:79559811-79560260	GM12891	blood:	n/a	chr4:79560020-79560029
30	TBP	chr4:79559460-79560220	GM12878	blood:	n/a	n/a
31	RELA	chr4:79558875-79560385	GM12891	blood:	n/a	n/a
32	RELA	chr4:79558877-79560347	GM19099	blood:	n/a	n/a
33	NFIC	chr4:79559392-79560273	GM12878	blood:	n/a	n/a
34	BCLAF1	chr4:79559663-79560327	GM12878	blood:	n/a	chr4:79560020-79560029
35	MTA3	chr4:79559408-79560332	GM12878	blood:	n/a	n/a
36	IRF4	chr4:79559732-79560228	GM12878	blood:	n/a	n/a
37	EP300	chr4:79559642-79560211	GM12878	blood:	n/a	chr4:79560125-79560139 chr4:79560020-79560034
38	RCOR1	chr4:79559450-79560283	GM12878	blood:	n/a	n/a
39	EP300	chr4:79559334-79560248	GM12878	blood:	n/a	chr4:79560125-79560139 chr4:79560020-79560034
40	EBF1	chr4:79559754-79560160	GM12878	blood:	n/a	n/a
41	CHD1	chr4:79559455-79560232	GM12878	blood:	n/a	n/a
42	MXI1	chr4:79559646-79560293	GM12878	blood:	n/a	n/a
43	RELA	chr4:79558843-79560361	GM12878	blood:	n/a	n/a
44	GATA1	chr4:79559615-79560321	PBDE	blood:	n/a	chr4:79560293-79560304 chr4:79560022-79560032
45	ZNF143	chr4:79559474-79560281	GM12878	blood:	n/a	n/a
46	MAX	chr4:79559534-79560237	GM12878	blood:	n/a	n/a
47	SPI1	chr4:79559426-79560345	GM12878	blood:	n/a	chr4:79560020-79560029
48	MAZ	chr4:79559592-79560171	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79557761..79562686-chr4:79563110..79568703,4	K562	blood:
2	chr4:79557978..79560128-chr4:79697718..79699238,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238816	TF binding region
ENSG00000251442	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10452151	1.00[AMR][1000 genomes]
rs55994157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56071306	1.00[AMR][1000 genomes]
rs56098630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57648305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57649400	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59700988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60681937	1.00[AMR][1000 genomes]
rs60950346	1.00[AMR][1000 genomes]
rs60998921	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61075598	1.00[AMR][1000 genomes]
rs61238857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828029	1.00[AMR][1000 genomes]
rs73828034	1.00[AMR][1000 genomes]
rs73828038	1.00[AMR][1000 genomes]
rs73828045	1.00[AMR][1000 genomes]
rs73828046	1.00[AMR][1000 genomes]
rs73828057	1.00[AMR][1000 genomes]
rs73828059	1.00[AMR][1000 genomes]
rs73828064	1.00[AMR][1000 genomes]
rs73828065	1.00[AMR][1000 genomes]
rs73828066	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828067	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828073	1.00[AMR][1000 genomes]
rs73828074	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828080	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828081	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828083	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828092	1.00[AMR][1000 genomes]
rs73828098	1.00[AMR][1000 genomes]
rs73828100	1.00[AMR][1000 genomes]
rs73828102	1.00[AMR][1000 genomes]
rs73830206	1.00[AMR][1000 genomes]
rs73830208	1.00[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	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79549600-79560000	Weak transcription	HMEC	breast
2	chr4:79550400-79564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:79551400-79578200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:79553000-79561600	Weak transcription	Placenta	Placenta
5	chr4:79553200-79563000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:79554000-79561600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:79555400-79562000	Weak transcription	Brain Substantia Nigra	brain
8	chr4:79555600-79564000	Weak transcription	Fetal Intestine Large	intestine
9	chr4:79555800-79566400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:79556000-79564000	Weak transcription	Brain Hippocampus Middle	brain
11	chr4:79557200-79568000	Enhancers	Primary B cells from cord blood	blood
12	chr4:79558400-79560800	Enhancers	Primary hematopoietic stem cells	blood
13	chr4:79558400-79561000	Enhancers	Primary B cells from peripheral blood	blood
14	chr4:79558800-79560200	Enhancers	Primary T cells from cord blood	blood
15	chr4:79558800-79560200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr4:79558800-79561200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:79559000-79560400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr4:79559000-79560400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:79559200-79560400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr4:79559200-79560400	Flanking Active TSS	GM12878-XiMat	blood
21	chr4:79559400-79560000	Enhancers	Duodenum Mucosa	Duodenum
22	chr4:79559400-79560200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr4:79559400-79560400	Enhancers	Dnd41	blood
24	chr4:79559400-79561000	Enhancers	Fetal Thymus	thymus
25	chr4:79559400-79561000	Enhancers	K562	blood
26	chr4:79559400-79561000	Enhancers	NHEK	skin
27	chr4:79559600-79560400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr4:79559800-79560000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr4:79559800-79560000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr4:79559800-79560200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr4:79559800-79560200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:79559800-79560400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr4:79559800-79564000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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