Variant report

Variant	rs58824375
Chromosome Location	chr19:55673145-55673146
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	E2F6	chr19:55672963-55673394	H1-hESC	embryonic stem cell:	n/a	chr19:55673196-55673206
2	MAX	chr19:55672980-55673763	H1-hESC	embryonic stem cell:	n/a	chr19:55673207-55673214
3	MAX	chr19:55672978-55673302	H1-hESC	embryonic stem cell:	n/a	chr19:55673207-55673214
4	E2F6	chr19:55671759-55673691	H1-hESC	embryonic stem cell:	n/a	chr19:55672795-55672807 chr19:55673196-55673206

No.	Distal block	Cell Line	Cell type
1	chr19:55627388..55629698-chr19:55672061..55673602,2	K562	blood:
2	chr19:55579852..55582710-chr19:55671936..55674879,2	K562	blood:
3	chr19:55669904..55673815-chr19:55917688..55921815,5	K562	blood:
4	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
5	chr19:55672196..55674741-chr19:55676544..55679173,3	K562	blood:
6	chr19:55666494..55670422-chr19:55672733..55675574,3	K562	blood:
7	chr19:55670813..55674787-chr19:55917654..55919984,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267110	TF binding region
DNAAF3	TF binding region
TNNI3	TF binding region
ENSG00000125503	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000267577	Chromatin interaction
ENSG00000129991	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000160439	Chromatin interaction
ENSG00000108106	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10421953	0.86[ASN][1000 genomes]
rs10423713	0.87[ASN][1000 genomes]
rs1128712	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12459688	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12459887	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12459917	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12459921	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12459930	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12460445	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12461148	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12461170	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12461195	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12461202	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12462211	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12463268	0.80[AMR][1000 genomes]
rs17458	0.88[AMR][1000 genomes]
rs2071572	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2071574	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2278281	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2288420	0.88[AMR][1000 genomes]
rs2288528	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2288529	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2301278	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3745922	0.88[AMR][1000 genomes]
rs3786867	0.95[ASN][1000 genomes]
rs3826887	0.91[AMR][1000 genomes]
rs3848618	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3859544	0.93[ASN][1000 genomes]
rs56666700	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56726774	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58017412	0.88[AMR][1000 genomes]
rs58218194	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59663064	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60176657	0.96[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60799292	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61570139	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7255625	0.96[ASN][1000 genomes]
rs890871	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9710458	0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55669600-55673400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr19:55670800-55673800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
3	chr19:55671600-55677600	Weak transcription	Right Atrium	heart
4	chr19:55671800-55677600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:55672000-55673400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:55672000-55673400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
7	chr19:55672000-55677200	Weak transcription	NHEK	skin
8	chr19:55672200-55673600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:55672200-55676800	Weak transcription	Hela-S3	cervix
10	chr19:55672400-55673200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr19:55672400-55673200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:55672400-55673400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:55672400-55673400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:55672600-55673400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:55672600-55673400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:55672600-55673600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:55672600-55677200	Weak transcription	Left Ventricle	heart
18	chr19:55672600-55677200	Weak transcription	Pancreas	Pancrea
19	chr19:55672800-55673400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
20	chr19:55672800-55673400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
21	chr19:55672800-55673400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:55672800-55673600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:55672800-55677000	Weak transcription	Right Ventricle	heart
24	chr19:55672800-55677000	Weak transcription	K562	blood
25	chr19:55673000-55673200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:55673000-55673200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:55673000-55673200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:55673000-55673200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:55673000-55673400	Bivalent Enhancer	Placenta	Placenta

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