Variant report

Variant	rs4858488
Chromosome Location	chr3:23314733-23314734
allele	A/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	FOXA1	chr3:23314402-23314772	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000206728	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1027380	0.95[ASN][1000 genomes]
rs11711630	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715107	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13087416	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13095887	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1390083	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1495133	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1495134	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1552931	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17342342	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2047340	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2055155	0.88[ASN][1000 genomes]
rs2088129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2132145	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2132147	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2132148	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2132149	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2201481	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2359760	0.85[EUR][1000 genomes]
rs36073188	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4293660	0.87[ASN][1000 genomes]
rs4334589	0.92[ASN][1000 genomes]
rs4858065	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858066	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858498	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6550751	0.87[AMR][1000 genomes]
rs6769959	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790185	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6799861	0.81[ASN][1000 genomes]
rs6806387	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73149661	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7618910	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7629327	0.93[ASN][1000 genomes]
rs7635882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636532	0.88[ASN][1000 genomes]
rs7648425	0.96[ASN][1000 genomes]
rs778493	0.81[EUR][1000 genomes]
rs903519	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs923996	0.80[AFR][1000 genomes]
rs9826103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9836135	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9840015	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844558	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848331	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 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	chr3:23295200-23321800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:23298800-23336600	Weak transcription	Thymus	Thymus
3	chr3:23302400-23321000	Weak transcription	Pancreas	Pancrea
4	chr3:23305600-23318400	Weak transcription	Brain Substantia Nigra	brain
5	chr3:23307200-23316000	Weak transcription	Primary B cells from cord blood	blood
6	chr3:23312000-23316800	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:23312400-23314800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:23313800-23316000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr3:23314000-23315800	Weak transcription	Lung	lung
10	chr3:23314000-23315800	Enhancers	NHLF	lung
11	chr3:23314000-23316400	Weak transcription	Right Ventricle	heart
12	chr3:23314000-23317000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:23314200-23315400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:23314200-23315600	Enhancers	NHDF-Ad	bronchial
15	chr3:23314200-23315600	Enhancers	Osteobl	bone
16	chr3:23314200-23315800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:23314400-23314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:23314400-23315000	Weak transcription	Primary T cells from cord blood	blood
19	chr3:23314400-23315800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:23314400-23315800	Enhancers	A549	lung
21	chr3:23314400-23317000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:23314400-23317400	Weak transcription	HSMM	muscle
23	chr3:23314400-23319400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:23314400-23330400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:23314600-23315000	Weak transcription	HSMMtube	muscle
26	chr3:23314600-23315200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:23314600-23315200	Weak transcription	GM12878-XiMat	blood
28	chr3:23314600-23315400	Enhancers	HMEC	breast
29	chr3:23314600-23318600	Weak transcription	Fetal Kidney	kidney

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