Variant report

Variant	rs1878045
Chromosome Location	chr19:51685315-51685316
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	MAX	chr19:51684949-51685614	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr19:51685271-51685718	NB4	blood:	n/a	n/a
3	SP1	chr19:51685032-51685603	H1-hESC	embryonic stem cell:	n/a	chr19:51685289-51685310 chr19:51685453-51685474 chr19:51685384-51685405
4	SIN3A	chr19:51685183-51685512	H1-hESC	embryonic stem cell:	n/a	n/a
5	NFYB	chr19:51685221-51685515	GM12878	blood:	n/a	chr19:51685383-51685398 chr19:51685258-51685268 chr19:51685288-51685302 chr19:51685451-51685463 chr19:51685452-51685466 chr19:51685385-51685395 chr19:51685256-51685271 chr19:51685256-51685270 chr19:51685454-51685464 chr19:51685288-51685301 chr19:51685287-51685299 chr19:51685290-51685300 chr19:51685288-51685303 chr19:51685452-51685467 chr19:51685383-51685398 chr19:51685290-51685300 chr19:51685383-51685397 chr19:51685256-51685271 chr19:51685452-51685467 chr19:51685288-51685303
6	MAX	chr19:51685058-51685709	H1-hESC	embryonic stem cell:	n/a	n/a
7	GTF2F1	chr19:51685237-51685587	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr19:51684645-51685774	H1-hESC	embryonic stem cell:	n/a	chr19:51685454-51685463 chr19:51685258-51685267 chr19:51685385-51685394 chr19:51685290-51685299
9	SP1	chr19:51685058-51685613	H1-hESC	embryonic stem cell:	n/a	chr19:51685289-51685310 chr19:51685453-51685474 chr19:51685384-51685405
10	POLR2A	chr19:51685306-51685723	NB4	blood:	n/a	n/a
11	MYC	chr19:51685253-51685686	NB4	blood:	n/a	n/a
12	MAX	chr19:51684666-51685669	H1-hESC	embryonic stem cell:	n/a	n/a
13	CHD2	chr19:51685141-51685601	H1-hESC	embryonic stem cell:	n/a	n/a
14	E2F6	chr19:51684902-51685686	H1-hESC	embryonic stem cell:	n/a	chr19:51685454-51685463 chr19:51685258-51685267 chr19:51685385-51685394 chr19:51685290-51685299
15	NFYB	chr19:51685173-51685627	K562	blood:	n/a	chr19:51685383-51685398 chr19:51685258-51685268 chr19:51685288-51685302 chr19:51685451-51685463 chr19:51685452-51685466 chr19:51685385-51685395 chr19:51685256-51685271 chr19:51685256-51685270 chr19:51685454-51685464 chr19:51685288-51685301 chr19:51685287-51685299 chr19:51685290-51685300 chr19:51685288-51685303 chr19:51685452-51685467 chr19:51685383-51685398 chr19:51685290-51685300 chr19:51685383-51685397 chr19:51685256-51685271 chr19:51685452-51685467 chr19:51685288-51685303
16	POLR2A	chr19:51685273-51685670	HL-60	blood:	n/a	n/a
17	MAFK	chr19:51685214-51685334	H1-hESC	embryonic stem cell:	n/a	n/a
18	CREB1	chr19:51685014-51685572	H1-hESC	embryonic stem cell:	n/a	n/a
19	BACH1	chr19:51685186-51685628	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SIGLEC20P	TF binding region
ENSG00000269072	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10404545	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10421703	0.80[AFR][1000 genomes]
rs10423943	0.80[AFR][1000 genomes]
rs1878046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28629968	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28662217	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34234198	1.00[EUR][1000 genomes]
rs3959246	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57285255	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59941188	0.80[AFR][1000 genomes]
rs60650416	0.83[AFR][1000 genomes]
rs60865290	0.80[AFR][1000 genomes]
rs61437908	0.80[AFR][1000 genomes]
rs7252160	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252364	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7252750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7254514	0.97[AFR][1000 genomes]
rs73610293	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73612702	0.80[AFR][1000 genomes]
rs73932855	0.89[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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51684600-51685800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:51684800-51685400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr19:51684800-51685600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:51684800-51687000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:51685000-51685400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:51685000-51685400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr19:51685000-51685400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
8	chr19:51685000-51685600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
9	chr19:51685000-51685600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr19:51685000-51688600	Enhancers	Primary hematopoietic stem cells	blood
11	chr19:51685200-51685400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:51685200-51685400	Bivalent Enhancer	Fetal Brain Female	brain
13	chr19:51685200-51685400	Bivalent Enhancer	Placenta	Placenta
14	chr19:51685200-51685400	Enhancers	Gastric	stomach
15	chr19:51685200-51685600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr19:51685200-51685600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:51685200-51685600	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr19:51685200-51685800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr19:51685200-51685800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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