Variant report

Variant	rs28549817
Chromosome Location	chr15:79268934-79268935
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	STAT5A	chr15:79268845-79270495	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:79268732-79273709	GM12891	blood:	n/a	n/a
3	MTA3	chr15:79268702-79270639	GM12878	blood:	n/a	n/a
4	ELF1	chr15:79268905-79269839	GM12878	blood:	n/a	chr15:79269198-79269209
5	PAX5	chr15:79268797-79270450	GM12878	blood:	n/a	chr15:79269545-79269554
6	CHD2	chr15:79268859-79270449	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:79268888-79273418	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:79268880-79270498	GM19193	blood:	n/a	n/a
9	POLR2A	chr15:79268749-79270549	GM12892	blood:	n/a	n/a
10	POLR2A	chr15:79268822-79270585	GM12892	blood:	n/a	n/a
11	RELA	chr15:79268795-79270520	GM10847	blood:	n/a	chr15:79269796-79269805 chr15:79269796-79269805
12	YY1	chr15:79268792-79269931	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:79268799-79270561	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:79264133..79265722-chr15:79266216..79269027,2	MCF-7	breast:
2	chr15:79266861..79270074-chr15:79272087..79274367,3	K562	blood:
3	chr1:145380838..145382385-chr15:79267640..79269976,2	MCF-7	breast:
4	chr15:79267805..79270419-chr15:79279866..79282392,3	MCF-7	breast:
5	chr15:79268574..79270778-chr15:79272295..79274532,2	K562	blood:

Variant related genes	Relation type
ENSG00000177699	TF binding region
ENSG00000233396	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12101364	1.00[EUR][1000 genomes]
rs16970387	0.81[EUR][1000 genomes]
rs28368520	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28391216	1.00[EUR][1000 genomes]
rs28407629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28427472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28461937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464364	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501391	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28501618	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28513164	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28516885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28546944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28547879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28557276	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28565526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28567804	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28587174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28603308	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28624404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28674868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28683537	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705105	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28709904	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28716558	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28718997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28722773	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28738778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9920807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904433	chr15:79243571-79310288	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79244000-79288000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr15:79261200-79280400	Weak transcription	Esophagus	oesophagus
3	chr15:79262600-79269000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:79263600-79269000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:79263600-79271200	Weak transcription	Lung	lung
6	chr15:79263800-79271200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:79264000-79271400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:79264200-79269600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:79264200-79269800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr15:79264200-79269800	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:79264200-79271400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:79264200-79271800	Weak transcription	Brain Angular Gyrus	brain
13	chr15:79264400-79269200	Weak transcription	HepG2	liver
14	chr15:79265800-79271000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:79268000-79269000	Enhancers	GM12878-XiMat	blood
16	chr15:79268200-79269000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr15:79268200-79272400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr15:79268400-79272600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr15:79268800-79269400	Enhancers	Brain Substantia Nigra	brain
20	chr15:79268800-79269400	Enhancers	Fetal Muscle Leg	muscle
21	chr15:79268800-79270600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:79268800-79273200	Enhancers	Primary B cells from peripheral blood	blood

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