Variant report

Variant	rs1356859
Chromosome Location	chr15:54792734-54792735
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10152437	0.85[CEU][hapmap]
rs10468008	0.88[CEU][hapmap]
rs11071082	0.89[CEU][hapmap]
rs11071084	0.89[CEU][hapmap]
rs11071087	0.88[CEU][hapmap]
rs11636139	0.84[JPT][hapmap]
rs11636568	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636573	0.92[CEU][hapmap]
rs11639005	0.88[CEU][hapmap]
rs11639014	0.88[CEU][hapmap]
rs11858004	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12148262	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs12437618	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs12442784	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12442847	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12443186	0.88[CEU][hapmap]
rs12595229	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs12907044	0.89[CEU][hapmap]
rs12916626	0.88[CEU][hapmap]
rs12917122	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1402112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851004	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414308	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs2414310	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414321	0.89[CEU][hapmap]
rs28675256	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2899541	0.85[CEU][hapmap]
rs34298302	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4457946	0.89[CEU][hapmap]
rs4506836	0.89[CEU][hapmap]
rs4641682	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774695	0.89[CEU][hapmap]
rs4774696	0.92[CEU][hapmap]
rs4776231	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs4776233	0.89[CEU][hapmap]
rs5017619	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs622459	0.92[JPT][hapmap]
rs6493681	0.84[JPT][hapmap]
rs7178299	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8023474	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap]
rs8023499	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8025195	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8027041	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8027984	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8032415	0.88[CEU][hapmap]
rs8033437	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8038538	0.89[CEU][hapmap]
rs8039515	0.88[CEU][hapmap]
rs885203	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs885204	0.92[CEU][hapmap]
rs9302181	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv904233	chr15:54703195-54797177	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv457153	chr15:54705902-54795040	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv569504	chr15:54705902-54795040	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv904235	chr15:54710873-54795040	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv569506	chr15:54715550-54796592	Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1038660	chr15:54756184-55039913	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1356859	TMEM229A	trans	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54775200-54794000	Weak transcription	Fetal Lung	lung
2	chr15:54777800-54810400	Weak transcription	Aorta	Aorta
3	chr15:54790800-54793200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr15:54790800-54793200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr15:54791000-54793000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr15:54791000-54793200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr15:54791000-54793200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr15:54791200-54792800	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr15:54791200-54792800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:54792200-54792800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:54792400-54792800	Weak transcription	H9 Cell Line	embryonic stem cell

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