Variant report

Variant	rs10940424
Chromosome Location	chr5:49897412-49897413
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	FOXA2	chr5:49897325-49897846	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000271455	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10038842	0.82[EUR][1000 genomes]
rs10041633	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10045122	0.85[EUR][1000 genomes]
rs10052001	0.97[EUR][1000 genomes]
rs10071272	0.87[EUR][1000 genomes]
rs10434558	0.87[EUR][1000 genomes]
rs10471940	0.82[EUR][1000 genomes]
rs10940423	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11738761	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739828	0.81[AFR][1000 genomes]
rs11741205	1.00[EUR][1000 genomes]
rs11745945	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12188654	0.82[EUR][1000 genomes]
rs12653803	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13159764	0.91[EUR][1000 genomes]
rs13162921	0.93[EUR][1000 genomes]
rs16884018	0.81[EUR][1000 genomes]
rs1839128	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1900738	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1972980	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2034392	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2034393	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2034394	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2121979	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2166893	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2166894	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2354526	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4101529	0.96[EUR][1000 genomes]
rs4282859	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4415044	0.94[EUR][1000 genomes]
rs4440312	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4572006	0.83[ASN][1000 genomes]
rs4865592	0.84[EUR][1000 genomes]
rs4865593	0.84[EUR][1000 genomes]
rs4865846	0.87[EUR][1000 genomes]
rs4865895	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4865896	0.96[EUR][1000 genomes]
rs57079776	0.81[EUR][1000 genomes]
rs6450292	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6450301	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6863162	0.83[ASN][1000 genomes]
rs6863575	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6867590	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6872070	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6879306	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6887758	0.83[ASN][1000 genomes]
rs6888147	0.97[EUR][1000 genomes]
rs7702541	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7709831	0.97[EUR][1000 genomes]
rs7710150	0.97[EUR][1000 genomes]
rs7721050	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7728222	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7730847	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7734389	0.82[EUR][1000 genomes]
rs7736142	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv964850	chr5:49883635-49942856	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv14399	chr5:49885912-49934455	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10940424	PARP8	Cis_1M	lymphoblastoid	RTeQTL
rs10940424	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49891400-49897600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:49891600-49897600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:49896000-49903400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:49896600-49898200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr5:49896800-49898200	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr5:49896800-49899000	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr5:49897000-49897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:49897200-49898200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr5:49897200-49898200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr5:49897200-49898200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:49897200-49898200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr5:49897400-49898000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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