Variant report

Variant	rs63710
Chromosome Location	chr5:57954311-57954312
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs149351	0.80[ASN][1000 genomes]
rs149525	0.80[ASN][1000 genomes]
rs158955	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs158957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs158958	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs158970	0.93[GIH][hapmap]
rs158974	0.90[GIH][hapmap]
rs158977	0.90[GIH][hapmap]
rs158980	0.82[JPT][hapmap]
rs158990	0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs158993	0.82[JPT][hapmap]
rs158997	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs158999	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs159000	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs159002	0.82[JPT][hapmap]
rs159003	0.90[ASN][1000 genomes]
rs159004	0.81[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs159006	0.90[ASN][1000 genomes]
rs159007	0.81[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs159008	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs169705	0.90[GIH][hapmap]
rs176637	0.80[ASN][1000 genomes]
rs186010	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2032815	0.91[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2161246	0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2591924	0.82[JPT][hapmap]
rs290572	0.82[JPT][hapmap]
rs292984	0.90[GIH][hapmap]
rs292985	0.90[GIH][hapmap]
rs293023	0.86[ASN][1000 genomes]
rs380850	0.90[GIH][hapmap]
rs9790998	0.81[JPT][hapmap]

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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1029145	chr5:57905821-58141221	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830311	chr5:57912546-58105636	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020937	chr5:57938969-57959918	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv4845	chr5:57949493-57994156	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2760929	chr5:57952586-57959954	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv1806916	chr5:57954311-57959223	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv1807554	chr5:57954311-57959223	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv437464	chr5:57954311-57961405	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv437465	chr5:57954311-57961405	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs63710	THSD4	trans	cerebellum	SCAN
rs63710	KIF2A	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57954000-57954600	Enhancers	Primary hematopoietic stem cells	blood
2	chr5:57954000-57954600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:57954000-57954800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr5:57954200-57954800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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