Variant report

Variant	rs1903778
Chromosome Location	chr11:6120908-6120909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10839509	0.81[EUR][1000 genomes]
rs10839510	0.81[EUR][1000 genomes]
rs10839512	0.81[EUR][1000 genomes]
rs10839513	0.81[EUR][1000 genomes]
rs11040741	0.81[EUR][1000 genomes]
rs11826453	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12360715	0.81[EUR][1000 genomes]
rs1381911	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1599692	1.00[ASN][1000 genomes]
rs1903779	0.81[ASN][1000 genomes]
rs325634	0.87[ASN][1000 genomes]
rs325639	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.94[ASN][1000 genomes]
rs325640	1.00[JPT][hapmap]
rs325657	0.83[ASN][1000 genomes]
rs325661	0.86[ASN][1000 genomes]
rs325666	0.92[ASN][1000 genomes]
rs325697	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34220108	0.86[ASN][1000 genomes]
rs34481020	0.81[EUR][1000 genomes]
rs35349232	0.81[EUR][1000 genomes]
rs3921908	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MKK][hapmap];1.00[ASN][1000 genomes]
rs4520575	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758078	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758085	1.00[ASN][1000 genomes]
rs4758086	0.89[ASN][1000 genomes]
rs4758380	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758392	0.94[ASN][1000 genomes]
rs5005636	0.81[EUR][1000 genomes]
rs5005637	0.81[EUR][1000 genomes]
rs5005638	0.80[EUR][1000 genomes]
rs6578740	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6578742	0.83[ASN][1000 genomes]
rs6578743	0.92[ASN][1000 genomes]
rs6578744	1.00[ASN][1000 genomes]
rs7110410	0.81[ASN][1000 genomes]
rs7117911	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7480133	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs7930953	0.89[ASN][1000 genomes]
rs7944650	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7948429	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	esv10302	chr11:6104402-6121639	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
6	esv9953	chr11:6114243-6122520	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a
7	nsv553356	chr11:6116038-6121077	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a
8	nsv553357	chr11:6116038-6121432	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	inside rSNPs	n/a
9	nsv553358	chr11:6116038-6121550	Bivalent Enhancer Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a
10	nsv553361	chr11:6116294-6121077	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a
11	nsv553362	chr11:6116776-6121006	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a
12	nsv553363	chr11:6116776-6121432	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	inside rSNPs	n/a
13	nsv553364	chr11:6116776-6121496	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	inside rSNPs	n/a
14	esv1823542	chr11:6116776-6121550	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	inside rSNPs	n/a
15	nsv553365	chr11:6116776-6121550	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	inside rSNPs	n/a
16	nsv553366	chr11:6116776-6125660	Enhancers Bivalent Enhancer Weak transcription	TF binding region	1 gene(s)	inside rSNPs	n/a
17	nsv553367	chr11:6116974-6121077	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a
18	nsv553368	chr11:6116974-6121432	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a
19	nsv553369	chr11:6116974-6121550	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a
20	esv1796383	chr11:6117526-6121550	Enhancers Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a
21	esv1800766	chr11:6117526-6121550	Bivalent Enhancer Enhancers	n/a	n/a	inside rSNPs	n/a
22	esv1830284	chr11:6117526-6121550	Enhancers Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1903778	OR52N2	cis	parietal	SCAN
rs1903778	OVCH2	cis	parietal	SCAN
rs1903778	DNHD1	cis	parietal	SCAN
rs1903778	TMEM9B	cis	parietal	SCAN
rs1903778	PPFIBP2	cis	cerebellum	SCAN
rs1903778	OR52N4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:6120400-6122000	Enhancers	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links