Variant report

Variant	rs28579596
Chromosome Location	chr4:79560312-79560313
allele	C/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	RELA	chr4:79558885-79560367	GM18951	blood:	n/a	n/a
2	RELA	chr4:79558837-79560320	GM10847	blood:	n/a	n/a
3	CHD2	chr4:79559680-79560344	GM12878	blood:	n/a	n/a
4	ATF2	chr4:79559350-79560346	GM12878	blood:	n/a	n/a
5	RELA	chr4:79558875-79560385	GM12891	blood:	n/a	n/a
6	RELA	chr4:79558877-79560347	GM19099	blood:	n/a	n/a
7	BCLAF1	chr4:79559663-79560327	GM12878	blood:	n/a	chr4:79560020-79560029
8	MTA3	chr4:79559408-79560332	GM12878	blood:	n/a	n/a
9	RELA	chr4:79558843-79560361	GM12878	blood:	n/a	n/a
10	GATA1	chr4:79559615-79560321	PBDE	blood:	n/a	chr4:79560293-79560304 chr4:79560022-79560032
11	SPI1	chr4:79559426-79560345	GM12878	blood:	n/a	chr4:79560020-79560029

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79549184..79553600-chr4:79560172..79565329,6	K562	blood:
2	chr4:79557761..79562686-chr4:79563110..79568703,4	K562	blood:

Variant related genes	Relation type
ENSG00000238816	TF binding region
ENSG00000251442	Chromatin interaction
ENSG00000200998	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10028815	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10029214	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10857035	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11098274	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11098275	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11098278	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11932080	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12510383	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12510411	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12639656	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12644222	0.81[ASN][1000 genomes]
rs12711028	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13110339	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1346145	0.80[AMR][1000 genomes]
rs1532427	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34636970	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4074675	0.86[AMR][1000 genomes]
rs4254805	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4495064	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4560439	0.80[AMR][1000 genomes]
rs4612	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4645238	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5944	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62308286	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533827	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533828	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6815367	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6817175	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6821449	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6822675	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6825328	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6842686	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6842723	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7656801	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7659978	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7675464	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7675646	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7677783	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699905	0.82[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	chr4:79550400-79564200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:79551400-79578200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:79553000-79561600	Weak transcription	Placenta	Placenta
4	chr4:79553200-79563000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:79554000-79561600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:79555400-79562000	Weak transcription	Brain Substantia Nigra	brain
7	chr4:79555600-79564000	Weak transcription	Fetal Intestine Large	intestine
8	chr4:79555800-79566400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:79556000-79564000	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:79557200-79568000	Enhancers	Primary B cells from cord blood	blood
11	chr4:79558400-79560800	Enhancers	Primary hematopoietic stem cells	blood
12	chr4:79558400-79561000	Enhancers	Primary B cells from peripheral blood	blood
13	chr4:79558800-79561200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:79559000-79560400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr4:79559000-79560400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:79559200-79560400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr4:79559200-79560400	Flanking Active TSS	GM12878-XiMat	blood
18	chr4:79559400-79560400	Enhancers	Dnd41	blood
19	chr4:79559400-79561000	Enhancers	Fetal Thymus	thymus
20	chr4:79559400-79561000	Enhancers	K562	blood
21	chr4:79559400-79561000	Enhancers	NHEK	skin
22	chr4:79559600-79560400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr4:79559800-79560400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr4:79559800-79564000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:79560000-79560400	Enhancers	HMEC	breast
26	chr4:79560000-79560400	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr4:79560000-79564000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr4:79560200-79561000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:79560200-79561000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:79560200-79564000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:79560200-79565200	Weak transcription	Primary T cells from cord blood	blood
32	chr4:79560200-79565400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:79560200-79565600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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