Variant report

Variant	rs10143148
Chromosome Location	chr14:39964127-39964128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10047876	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10130181	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10133746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10134065	0.81[ASN][1000 genomes]
rs10136490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10136915	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10140997	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs10142029	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10144377	0.91[AFR][1000 genomes]
rs10145757	0.82[AFR][1000 genomes]
rs10146106	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10146622	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10220689	1.00[CHB][hapmap]
rs10483538	0.91[AFR][1000 genomes]
rs12431558	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12431815	0.86[ASN][1000 genomes]
rs12433987	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12434300	0.85[ASN][1000 genomes]
rs17109168	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap]
rs17622868	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1955716	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1998885	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1998886	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2103795	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2179973	0.88[ASN][1000 genomes]
rs2415541	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs28398804	0.88[ASN][1000 genomes]
rs28419351	0.88[ASN][1000 genomes]
rs28454173	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28568594	0.88[ASN][1000 genomes]
rs28704775	0.88[ASN][1000 genomes]
rs28871954	0.88[ASN][1000 genomes]
rs2899887	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs3783291	0.82[CHB][hapmap]
rs4316662	0.91[AFR][1000 genomes]
rs4902559	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs59804731	0.86[ASN][1000 genomes]
rs61999073	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs61999077	0.88[ASN][1000 genomes]
rs61999079	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62000686	0.82[AFR][1000 genomes]
rs62000696	0.91[AFR][1000 genomes]
rs62000708	0.91[AFR][1000 genomes]
rs62000709	0.91[AFR][1000 genomes]
rs62000711	0.91[AFR][1000 genomes]
rs62000715	0.91[AFR][1000 genomes]
rs62001106	0.88[ASN][1000 genomes]
rs62015674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62015677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62017271	0.86[ASN][1000 genomes]
rs7146753	0.88[ASN][1000 genomes]
rs7156962	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7158282	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7161482	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8006076	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs8007769	0.86[ASN][1000 genomes]
rs9322999	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9805937	1.00[CHB][hapmap];0.82[JPT][hapmap]

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	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv832774	chr14:39897746-40060823	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv915558	chr14:39944831-40165370	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv456212	chr14:39957437-40096888	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv564418	chr14:39957437-40096888	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10143148	CTAGE5	cis	parietal	SCAN
rs10143148	HSS00041593	cis	multi-tissue	Pritchard
rs10143148	FBXO33	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39958200-39964800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr14:39958200-39968600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:39961400-39966400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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