Variant report

Variant	rs11186320
Chromosome Location	chr10:92576448-92576449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
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];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10881838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10881839	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10881844	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[ASN][1000 genomes]
rs11186324	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11186350	0.90[ASN][1000 genomes]
rs11186351	0.83[CEU][hapmap];0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs11597471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[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]
rs11599902	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]
rs12246757	0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12254390	0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12259060	0.98[AMR][1000 genomes];0.99[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];0.94[ASN][1000 genomes]
rs12259401	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35987367	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4520504	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4522081	0.84[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4568910	0.84[ASN][1000 genomes]
rs4933618	0.84[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs6583737	0.90[ASN][1000 genomes]
rs66650915	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7080463	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7082401	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7087400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7089472	0.84[ASN][1000 genomes]
rs7101301	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7896973	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs7900048	0.84[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs7905446	0.90[ASN][1000 genomes]
rs7906960	0.98[AMR][1000 genomes];0.99[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];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467433	chr10:92083015-92598458	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv551880	chr10:92083015-92598458	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS 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	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
4	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
5	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
6	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
7	nsv1054504	chr10:92099335-92590723	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv533133	chr10:92363552-92594891	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11186320	GPR120	cis	cerebellum	SCAN
rs11186320	KIF20B	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:92573000-92577200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:92573800-92576800	Enhancers	HMEC	breast
3	chr10:92574000-92577400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr10:92574200-92577000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:92574800-92579400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr10:92574800-92581200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr10:92575200-92576600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr10:92575200-92576800	Enhancers	NHEK	skin
9	chr10:92575400-92576600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:92575400-92576600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:92575400-92577400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:92575600-92576800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr10:92575600-92577600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr10:92575800-92577000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr10:92575800-92578200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr10:92575800-92579200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr10:92576000-92581200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr10:92576200-92576600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr10:92576400-92576600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr10:92576400-92577000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr10:92576400-92577200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr10:92576400-92577200	Enhancers	Primary hematopoietic stem cells	blood
23	chr10:92576400-92577400	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links