Variant report

Variant	rs11599902
Chromosome Location	chr10:92598823-92598824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10785972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881844	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.89[ASN][1000 genomes]
rs11186320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11186324	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11186350	0.92[ASN][1000 genomes]
rs11186351	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs11597471	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246757	0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs12254390	0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs12259060	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12259062	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12259401	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35987367	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520504	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522081	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4568910	0.86[ASN][1000 genomes]
rs4933618	0.84[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs6583737	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66650915	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7080463	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7082401	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7087400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7089472	0.86[ASN][1000 genomes]
rs7101301	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs7896973	0.84[CEU][hapmap];0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs7900048	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7905446	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7906960	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7909232	0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]

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	nsv516743	chr10:92083015-92605119	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1049931	chr10:92083932-92605364	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv948363	chr10:92084520-92614402	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv551882	chr10:92090785-92598823	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1036058	chr10:92471568-92605364	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv831945	chr10:92590576-92793582	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11599902	KIF20B	cis	parietal	SCAN
rs11599902	GPR120	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:92584200-92602400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr10:92597600-92599600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:92597800-92599200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:92597800-92599200	Weak transcription	HMEC	breast
5	chr10:92597800-92599400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:92597800-92599400	Weak transcription	NHEK	skin
7	chr10:92597800-92616200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:92598600-92599400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr10:92598800-92599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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