Variant report

Variant	rs1599176
Chromosome Location	chr5:113791291-113791292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10519384	0.83[ASW][hapmap];0.82[LWK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs12515458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12719181	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13153326	0.86[ASN][1000 genomes]
rs13154435	0.82[ASN][1000 genomes]
rs13154738	0.82[ASN][1000 genomes]
rs13156054	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13156389	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1459782	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459783	0.85[LWK][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs1459789	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17136666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1841248	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1975851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2125772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2125773	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34484477	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34512774	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35211026	0.99[EUR][1000 genomes]
rs35386131	0.82[ASN][1000 genomes]
rs35495721	0.82[ASN][1000 genomes]
rs35641030	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3891371	0.82[ASN][1000 genomes]
rs4466150	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4705506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4705671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6889371	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.99[EUR][1000 genomes]
rs7730205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs898354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs898355	0.82[YRI][hapmap]
rs977850	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830451	chr5:113684301-113829833	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv882729	chr5:113743628-114497708	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1599176	TSSK1B	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:113786200-113793200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:113786400-113791600	Weak transcription	Brain Hippocampus Middle	brain
3	chr5:113786400-113793000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:113786400-113793000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:113786400-113793000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:113786600-113793200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr5:113786600-113793200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:113786600-113793400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:113788400-113793200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:113788600-113792800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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