Variant report

Variant	rs4515838
Chromosome Location	chr1:120040976-120040977
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	FOXA2	chr1:120040426-120041060	A549	lung:	n/a	n/a

Variant related genes	Relation type
GAPDHP58	TF binding region

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1047303	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10733103	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10737750	0.86[EUR][1000 genomes]
rs10737751	0.86[EUR][1000 genomes]
rs10737753	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10737754	0.84[EUR][1000 genomes]
rs10754397	0.92[EUR][1000 genomes]
rs10754400	0.86[EUR][1000 genomes]
rs10754401	0.86[EUR][1000 genomes]
rs10754402	0.85[EUR][1000 genomes]
rs10754403	0.85[EUR][1000 genomes]
rs10754404	0.85[EUR][1000 genomes]
rs10754405	0.84[EUR][1000 genomes]
rs10754406	0.84[EUR][1000 genomes]
rs10754407	0.84[EUR][1000 genomes]
rs10754408	0.84[EUR][1000 genomes]
rs10754409	0.82[EUR][1000 genomes]
rs10802100	0.82[EUR][1000 genomes]
rs10802101	0.92[EUR][1000 genomes]
rs10802108	0.85[EUR][1000 genomes]
rs10802109	0.84[EUR][1000 genomes]
rs10802110	0.84[EUR][1000 genomes]
rs10802111	0.84[EUR][1000 genomes]
rs10923838	0.90[EUR][1000 genomes]
rs10923839	0.91[EUR][1000 genomes]
rs10923844	0.86[EUR][1000 genomes]
rs10923845	0.84[EUR][1000 genomes]
rs10923848	0.85[EUR][1000 genomes]
rs10923850	0.84[EUR][1000 genomes]
rs10923852	0.83[EUR][1000 genomes]
rs10923853	0.84[EUR][1000 genomes]
rs12035199	0.90[ASN][1000 genomes]
rs12084925	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12117401	0.82[EUR][1000 genomes]
rs12139993	0.89[EUR][1000 genomes]
rs12403142	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13374289	0.84[EUR][1000 genomes]
rs1341008	0.81[EUR][1000 genomes]
rs1812256	0.86[EUR][1000 genomes]
rs1856888	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1885001	0.85[EUR][1000 genomes]
rs1977208	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1983726	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1987612	0.84[EUR][1000 genomes]
rs1998181	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1998182	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2009240	0.84[EUR][1000 genomes]
rs2010580	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2010807	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2011178	0.92[EUR][1000 genomes]
rs2011191	0.92[EUR][1000 genomes]
rs2064901	0.90[EUR][1000 genomes]
rs2064902	0.91[EUR][1000 genomes]
rs2093189	0.98[EUR][1000 genomes]
rs2104039	0.98[EUR][1000 genomes]
rs2208379	0.84[EUR][1000 genomes]
rs2208380	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208381	0.84[EUR][1000 genomes]
rs2208382	0.84[EUR][1000 genomes]
rs2224397	0.84[EUR][1000 genomes]
rs2224398	0.84[EUR][1000 genomes]
rs2224399	0.84[EUR][1000 genomes]
rs2236780	0.81[EUR][1000 genomes]
rs2362814	0.85[EUR][1000 genomes]
rs2362815	0.85[EUR][1000 genomes]
rs2362816	0.84[EUR][1000 genomes]
rs2362817	0.84[EUR][1000 genomes]
rs2362818	0.84[EUR][1000 genomes]
rs2362820	0.84[EUR][1000 genomes]
rs2362821	0.84[EUR][1000 genomes]
rs2885612	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2885613	0.84[EUR][1000 genomes]
rs2885614	0.84[EUR][1000 genomes]
rs3737652	0.84[EUR][1000 genomes]
rs3737653	0.84[EUR][1000 genomes]
rs3765945	0.98[EUR][1000 genomes]
rs4233454	0.84[EUR][1000 genomes]
rs4478857	0.86[EUR][1000 genomes]
rs4659007	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4659008	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4659009	0.84[EUR][1000 genomes]
rs4659182	0.92[EUR][1000 genomes]
rs4659191	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4659192	0.84[EUR][1000 genomes]
rs4659194	0.84[EUR][1000 genomes]
rs4659195	0.81[EUR][1000 genomes]
rs4659196	0.81[EUR][1000 genomes]
rs5009592	0.84[EUR][1000 genomes]
rs5012379	0.84[EUR][1000 genomes]
rs6428829	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6428830	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657934	0.84[EUR][1000 genomes]
rs6662380	0.85[EUR][1000 genomes]
rs6663497	0.84[EUR][1000 genomes]
rs6667572	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6667901	0.98[EUR][1000 genomes]
rs6668680	0.84[EUR][1000 genomes]
rs6668763	0.84[EUR][1000 genomes]
rs6681580	0.84[EUR][1000 genomes]
rs6684302	0.84[EUR][1000 genomes]
rs6684370	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6686779	0.98[EUR][1000 genomes]
rs6691637	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515615	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7517005	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7534643	0.96[EUR][1000 genomes]
rs7536990	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7539594	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs911241	0.92[EUR][1000 genomes]
rs911244	0.88[ASN][1000 genomes]
rs911245	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs927208	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs951693	0.85[EUR][1000 genomes]
rs9659330	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9659331	0.84[EUR][1000 genomes]
rs971058	0.84[EUR][1000 genomes]
rs9887805	0.84[EUR][1000 genomes]
rs9887874	0.84[EUR][1000 genomes]
rs9887882	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	esv2763647	chr1:119929442-120154798	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	esv2757749	chr1:120016696-120214577	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	esv2758964	chr1:120016696-120214577	Enhancers ZNF genes & repeats Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv524727	chr1:120023971-120056401	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv946183	chr1:120038341-120047756	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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