Variant report

Variant	rs203545
Chromosome Location	chr20:1195688-1195689
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs203537	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs203538	0.96[ASN][1000 genomes]
rs203541	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs203542	0.97[ASN][1000 genomes]
rs203543	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203547	0.98[ASN][1000 genomes]
rs203548	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203549	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203550	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203555	0.83[ASN][1000 genomes]
rs203556	0.81[CHD][hapmap]
rs396004	0.92[ASN][1000 genomes]
rs397020	0.88[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs430731	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs446359	0.90[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	nsv531450	chr20:809607-1221836	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1058524	chr20:821434-1254865	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544138	chr20:821434-1254865	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1057939	chr20:824980-1316778	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv912585	chr20:992713-1210647	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1057097	chr20:1030940-1314265	Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs203545	LMF1	trans	parietal	SCAN
rs203545	TBC1D20	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1194000-1195800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr20:1194000-1195800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr20:1194000-1196000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr20:1194000-1197200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr20:1194400-1196000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr20:1194400-1196400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr20:1195200-1198800	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr20:1195400-1196200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr20:1195400-1197800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr20:1195600-1196000	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr20:1195600-1196200	Enhancers	Primary T cells from cord blood	blood
12	chr20:1195600-1196600	Enhancers	Primary hematopoietic stem cells	blood
13	chr20:1195600-1196600	Flanking Active TSS	K562	blood
14	chr20:1195600-1197400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr20:1195600-1197600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr20:1195600-1198600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr20:1195600-1198600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr20:1195600-1198800	Enhancers	Primary T helper 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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