Variant report

Variant	rs10789466
Chromosome Location	chr1:45991836-45991837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr1:45991790-45992219	HepG2	liver:	n/a	n/a
2	FOXA2	chr1:45991680-45992247	A549	lung:	n/a	n/a
3	FOXA1	chr1:45991810-45992245	T-47D	breast:	n/a	n/a
4	MAFK	chr1:45991835-45992303	HepG2	liver:	n/a	n/a
5	EP300	chr1:45991799-45992187	HepG2	liver:	n/a	n/a
6	FOXA1	chr1:45991731-45992326	HepG2	liver:	n/a	n/a
7	FOXA2	chr1:45991811-45992599	HepG2	liver:	n/a	n/a
8	SP1	chr1:45991802-45992213	HepG2	liver:	n/a	n/a
9	USF1	chr1:45991832-45992026	HepG2	liver:	n/a	chr1:45991935-45991946

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45990085..45992504-chr1:45996653..45999903,3	MCF-7	breast:
2	chr1:45805140..45807328-chr1:45987853..45992059,3	K562	blood:
3	chr1:45990878..45992460-chr1:46016513..46018764,2	K562	blood:
4	chr1:45990201..45992328-chr1:46015000..46016873,3	MCF-7	breast:
5	chr1:45984791..45989119-chr1:45989451..45994043,12	MCF-7	breast:
6	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
7	chr1:45990531..45992358-chr1:46014805..46016386,2	K562	blood:
8	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
9	chr1:45284051..45285694-chr1:45989373..45992080,2	K562	blood:
10	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:

No data

Variant related genes	Relation type
HMGB1P48	TF binding region
PRDX1	TF binding region
ENSG00000117448	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000117450	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10157597	0.94[EUR][1000 genomes]
rs1044717	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10736426	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1088099	0.93[EUR][1000 genomes]
rs11211132	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11211134	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12038608	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12048936	0.86[EUR][1000 genomes]
rs12082256	0.86[EUR][1000 genomes]
rs12145526	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12729974	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12749658	0.94[EUR][1000 genomes]
rs1337902	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1494813	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1974271	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2077808	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2152077	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2356555	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2356560	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2356561	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2991966	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2993257	0.92[EUR][1000 genomes]
rs2993259	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34315657	0.85[EUR][1000 genomes]
rs3748643	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4233498	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4660306	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4660309	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4660860	0.93[EUR][1000 genomes]
rs4660862	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4660864	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4660866	0.83[EUR][1000 genomes]
rs4660867	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4660868	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4660871	0.86[EUR][1000 genomes]
rs4660872	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6429567	0.93[EUR][1000 genomes]
rs6429569	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6667191	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6688424	0.93[EUR][1000 genomes]
rs6688516	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7516006	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7522705	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7534467	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7536557	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7539253	0.89[EUR][1000 genomes]
rs7543076	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7546268	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7549093	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs781066	0.92[EUR][1000 genomes]
rs882803	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937290	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs945179	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9725380	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9803979	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10789466	CCDC163P	cis	lung	GTEx
rs10789466	CCDC163P	cis	Nerve Tibial	GTEx
rs10789466	CCDC163P	cis	Stomach	GTEx
rs10789466	CCDC163P	cis	Esophagus Mucosa	GTEx
rs10789466	CCDC163P	cis	Artery Aorta	GTEx
rs10789466	CCDC163P	cis	Thyroid	GTEx
rs10789466	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs10789466	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs10789466	CCDC163P	cis	Artery Tibial	GTEx
rs10789466	CCDC163P	cis	Muscle Skeletal	GTEx
rs10789466	CCDC163P	cis	Heart Left Ventricle	GTEx
rs10789466	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs10789466	CCDC163P	cis	Esophagus Muscularis	GTEx
rs10789466	CCDC163P	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45988200-45992200	Weak transcription	Fetal Lung	lung
2	chr1:45988200-45993000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:45988400-45992200	Weak transcription	Fetal Intestine Large	intestine
4	chr1:45988400-45992200	Weak transcription	Fetal Kidney	kidney
5	chr1:45988400-45993400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:45988400-45997200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:45988600-45992200	Weak transcription	Fetal Heart	heart
8	chr1:45988600-45992200	Weak transcription	Fetal Intestine Small	intestine
9	chr1:45988600-45993400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:45989000-45993200	Weak transcription	Placenta	Placenta
11	chr1:45989200-46000600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:45990400-45992400	Enhancers	Hela-S3	cervix
13	chr1:45990400-45992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:45990400-45992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:45990600-45992200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:45990600-45992800	Enhancers	Stomach Mucosa	stomach
17	chr1:45990600-45992800	Enhancers	HepG2	liver
18	chr1:45991000-45992200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:45991000-45992400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:45991000-45993400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:45991000-45993400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:45991000-45993400	Weak transcription	K562	blood
23	chr1:45991200-45992000	Enhancers	A549	lung
24	chr1:45991200-45992200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:45991200-45992400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:45991200-45993400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:45991200-45993400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:45991400-45992000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:45991600-45992400	Enhancers	Liver	Liver

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