Variant report

Variant	rs199999
Chromosome Location	chr5:8700487-8700488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs169239	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187964	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs199181	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs199997	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs199998	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200000	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200001	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200003	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200006	0.81[AMR][1000 genomes]
rs200008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200009	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200010	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200011	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200012	1.00[ASN][1000 genomes]
rs200013	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs200014	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs200015	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs200017	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs200018	0.99[ASN][1000 genomes]
rs200036	0.99[ASN][1000 genomes]
rs200037	0.99[ASN][1000 genomes]
rs200038	0.99[ASN][1000 genomes]
rs200039	0.99[ASN][1000 genomes]
rs200040	0.99[ASN][1000 genomes]
rs200043	0.99[ASN][1000 genomes]
rs200044	0.99[ASN][1000 genomes]
rs200046	0.99[ASN][1000 genomes]
rs200047	0.99[ASN][1000 genomes]
rs200048	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs200049	0.99[ASN][1000 genomes]
rs200050	0.97[ASN][1000 genomes]
rs200052	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs200053	0.97[ASN][1000 genomes]
rs200064	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs200066	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs200068	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs200069	0.95[ASN][1000 genomes]
rs200095	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2519880	0.99[ASN][1000 genomes]
rs2651645	0.99[ASN][1000 genomes]
rs2963389	0.91[JPT][hapmap]
rs976987	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032346	chr5:8522331-8747061	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv537636	chr5:8522331-8747061	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1033498	chr5:8554438-8702228	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv537637	chr5:8690735-8730509	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
5	nsv881428	chr5:8697444-8715139	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
6	nsv881307	chr5:8697444-8718172	Weak transcription Active TSS Enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
7	nsv1016033	chr5:8699765-8747142	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
8	nsv436977	chr5:8699765-8749282	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv461931	chr5:8700487-8770185	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv597030	chr5:8700487-8770185	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs199999	SRD5A1	cis	cerebellum	SCAN
rs199999	PAPD7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:8696800-8700800	Weak transcription	Fetal Stomach	stomach
2	chr5:8699600-8702200	Enhancers	Fetal Lung	lung
3	chr5:8700000-8701800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:8700400-8700600	Enhancers	NHLF	lung
5	chr5:8700400-8701600	Enhancers	Fetal Muscle Leg	muscle
6	chr5:8700400-8701600	Enhancers	Ovary	ovary

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