Variant report

Variant	rs10519354
Chromosome Location	chr5:112689650-112689651
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10037429	1.00[CHB][hapmap]
rs10519348	1.00[CHB][hapmap]
rs11241202	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11738347	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11738587	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11740807	1.00[ASN][1000 genomes]
rs11741176	1.00[ASN][1000 genomes]
rs11741860	1.00[ASN][1000 genomes]
rs11746828	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11748646	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750254	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11750752	1.00[ASN][1000 genomes]
rs13161610	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs13161969	0.91[CEU][hapmap]
rs13162970	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13166822	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs13177178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13182359	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs1318772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13188803	0.83[ASN][1000 genomes]
rs13189851	0.87[EUR][1000 genomes]
rs164252	1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs17324474	0.87[EUR][1000 genomes]
rs17325908	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs17326496	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs17327139	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs182988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs185336	0.89[EUR][1000 genomes]
rs2120348	1.00[CHB][hapmap]
rs2545359	0.81[EUR][1000 genomes]
rs2545360	0.81[EUR][1000 genomes]
rs255857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs255859	0.93[EUR][1000 genomes]
rs255870	0.89[EUR][1000 genomes]
rs255871	0.93[EUR][1000 genomes]
rs26962	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs26965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs26980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26984	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26986	0.89[EUR][1000 genomes]
rs26989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs26990	1.00[CHB][hapmap]
rs2860483	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs34361144	0.93[EUR][1000 genomes]
rs34437714	0.91[ASN][1000 genomes]
rs34441430	0.83[ASN][1000 genomes]
rs34539248	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34614757	0.83[ASN][1000 genomes]
rs34625553	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs348919	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs348935	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs348939	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs35111059	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35352601	1.00[ASN][1000 genomes]
rs35451724	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35568473	0.89[EUR][1000 genomes]
rs36120874	0.83[ASN][1000 genomes]
rs36611	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs36613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs414475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs421515	0.89[EUR][1000 genomes]
rs446272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs458055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs4705554	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs4705829	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs58833244	1.00[ASN][1000 genomes]
rs66629800	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66957398	1.00[ASN][1000 genomes]
rs67344014	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67767339	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67894881	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68189049	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861939	1.00[CHB][hapmap]
rs71577443	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788641	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72797916	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10519354	TMEM232	cis	cerebellum	SCAN
rs10519354	CBS	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112667200-112693400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:112682000-112700000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:112688800-112690200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:112689000-112693200	Weak transcription	Left Ventricle	heart
5	chr5:112689200-112689800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:112689200-112690000	Enhancers	Fetal Heart	heart
7	chr5:112689400-112690000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:112689400-112690200	Enhancers	HMEC	breast
9	chr5:112689600-112690200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:112689600-112690200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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