Variant report

Variant	rs55990593
Chromosome Location	chr17:33794859-33794860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11651218	1.00[ASN][1000 genomes]
rs11654381	1.00[ASN][1000 genomes]
rs11657050	1.00[ASN][1000 genomes]
rs12949518	1.00[ASN][1000 genomes]
rs1838148	1.00[ASN][1000 genomes]
rs34658850	1.00[ASN][1000 genomes]
rs35077171	1.00[ASN][1000 genomes]
rs62078112	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825923	1.00[ASN][1000 genomes]
rs72825924	1.00[ASN][1000 genomes]
rs72825932	1.00[ASN][1000 genomes]
rs72825958	1.00[ASN][1000 genomes]
rs9898870	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055936	chr17:33327166-33884184	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer 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	112 gene(s)	inside rSNPs	diseases
2	nsv543317	chr17:33327166-33884184	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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	112 gene(s)	inside rSNPs	diseases
3	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv574741	chr17:33552275-33827134	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv1056116	chr17:33691457-33815452	Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv3432530	chr17:33738621-33802241	Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55990593	SLFN13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33791200-33801200	Weak transcription	Dnd41	blood
2	chr17:33793800-33797000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr17:33793800-33797000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:33793800-33797400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr17:33794000-33796000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr17:33794000-33796200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr17:33794000-33796800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr17:33794000-33797200	Enhancers	Hela-S3	cervix
9	chr17:33794000-33797400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:33794200-33796000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr17:33794200-33796200	Enhancers	Primary T cells from cord blood	blood
12	chr17:33794200-33796200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr17:33794200-33797000	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr17:33794400-33796200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr17:33794600-33795000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:33794600-33796000	Enhancers	Fetal Thymus	thymus
17	chr17:33794600-33797600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr17:33794800-33795400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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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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