Variant report

Variant	rs11228976
Chromosome Location	chr11:57030962-57030963
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10501367	0.86[GIH][hapmap]
rs10792083	0.96[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs10792085	0.84[CEU][hapmap]
rs10896595	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896597	0.94[ASN][1000 genomes]
rs10896599	0.86[ASN][1000 genomes]
rs10896602	0.84[CEU][hapmap]
rs11228968	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228975	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228978	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228980	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11228984	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs11228985	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11228988	0.86[EUR][1000 genomes]
rs11544374	0.86[GIH][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs11600878	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11604373	0.82[EUR][1000 genomes]
rs11604560	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11604778	0.84[ASN][1000 genomes]
rs11605053	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11607817	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419065	0.89[ASN][1000 genomes]
rs12421633	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421755	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12792781	0.84[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.95[ASN][1000 genomes]
rs12797769	0.96[ASN][1000 genomes]
rs17572970	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17651610	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17652078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892963	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892964	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1939489	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1939495	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2155231	0.89[ASN][1000 genomes]
rs2226613	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276038	0.82[JPT][hapmap]
rs2511026	0.85[ASN][1000 genomes]
rs2511029	0.89[ASN][1000 genomes]
rs2511030	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2846042	0.94[ASN][1000 genomes]
rs2846049	0.83[ASN][1000 genomes]
rs2846050	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2846051	0.87[ASN][1000 genomes]
rs2851722	0.94[ASN][1000 genomes]
rs35610294	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3935068	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4384399	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4565915	0.95[ASN][1000 genomes]
rs479949	0.94[ASN][1000 genomes]
rs4938855	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938857	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938859	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4938861	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4939132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs499318	0.94[ASN][1000 genomes]
rs5012051	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs519277	0.94[ASN][1000 genomes]
rs522656	0.89[ASN][1000 genomes]
rs528101	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58295319	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs590240	0.89[ASN][1000 genomes]
rs599947	0.89[ASN][1000 genomes]
rs625565	0.94[ASN][1000 genomes]
rs652016	0.92[ASN][1000 genomes]
rs654635	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6591408	0.82[YRI][hapmap]
rs6591413	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591415	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6591416	0.95[ASN][1000 genomes]
rs6591417	0.95[ASN][1000 genomes]
rs7102963	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119375	0.86[GIH][hapmap]
rs7120644	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128371	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7130252	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72921992	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7935236	0.91[ASN][1000 genomes]
rs7943761	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11228976	GLYATL2	cis	parietal	SCAN
rs11228976	OR8U1	cis	parietal	SCAN
rs11228976	OR5AN1	cis	parietal	SCAN
rs11228976	OR5T1	cis	cerebellum	SCAN
rs11228976	OR4C6	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57029400-57031600	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr11:57029400-57031600	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr11:57030400-57031000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr11:57030400-57031400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr11:57030400-57031600	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr11:57030600-57031000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:57030600-57031200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr11:57030600-57036800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:57030800-57031000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr11:57030800-57031000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:57030800-57031200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr11:57030800-57031200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr11:57030800-57031600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr11:57030800-57031600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links