Variant report

Variant	rs10038239
Chromosome Location	chr5:17797640-17797641
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10039437	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10041245	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10041264	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10064153	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10065766	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1443399	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1514864	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1514865	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1813047	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2380154	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2380155	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2380156	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2890350	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3860739	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6451456	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6890888	0.81[ASN][1000 genomes]
rs6890889	0.80[ASN][1000 genomes]
rs7443766	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7444529	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7444677	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7445380	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7446821	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7447894	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7448499	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7448643	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7448664	0.80[EUR][1000 genomes]
rs7705830	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7707669	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7712254	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7712426	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7722577	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7722582	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7728224	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879042	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9292808	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs971715	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757986	chr5:17364700-17936404	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	esv2759328	chr5:17364700-17936404	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	esv2757108	chr5:17398090-17804346	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv10674	chr5:17495989-17799341	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv880367	chr5:17599577-17889537	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv881550	chr5:17599577-17922072	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv1034288	chr5:17601541-17873638	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv469893	chr5:17604088-17803243	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv428820	chr5:17604088-17803243	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1025295	chr5:17647950-17807484	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv537678	chr5:17647950-17807484	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv597361	chr5:17662955-17799807	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv880263	chr5:17697797-17953026	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv881366	chr5:17715854-17842564	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv881518	chr5:17715854-18011718	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv469764	chr5:17721852-17880830	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv482614	chr5:17721852-17880830	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv532770	chr5:17727030-18415622	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv432725	chr5:17764192-17981553	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv1025965	chr5:17780459-17799400	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv880810	chr5:17788303-17828116	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10038239	FBXL7	cis	parietal	SCAN
rs10038239	KIAA1161	trans	parietal	SCAN
rs10038239	BASP1	cis	cerebellum	SCAN
rs10038239	LOC285696	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17796200-17797800	Enhancers	Hela-S3	cervix
2	chr5:17796400-17797800	Enhancers	HMEC	breast
3	chr5:17796600-17801800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:17796800-17797800	Enhancers	HUVEC	blood vessel
5	chr5:17797400-17797800	Flanking Active TSS	A549	lung
6	chr5:17797600-17802600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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