Variant report

Variant	rs11040261
Chromosome Location	chr11:49156039-49156040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOLH1-1	chr11:49155205-49156352	NONHSAT021310

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10839217	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10839230	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11040241	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11040255	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11040289	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11822117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs11826051	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12271751	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1819409	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap]
rs1847640	0.92[ASW][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.92[YRI][hapmap]
rs191862	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs202672	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs202673	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs202681	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs202687	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs202689	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs202695	0.94[ASN][1000 genomes]
rs202696	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202698	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs202701	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs202705	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs202713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs202719	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs202724	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs369803	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58846727	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs595139	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs613450	0.81[ASN][1000 genomes]
rs648728	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs651278	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs689329	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7932738	0.85[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.89[LWK][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759824	chr11:48303671-49185190	Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	esv1828260	chr11:48735614-49162948	Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv427886	chr11:48850348-49185190	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv2758268	chr11:48856977-49185190	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv469956	chr11:48922645-49862647	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv832145	chr11:49002873-49185190	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv897484	chr11:49042866-49162948	ZNF genes & repeats Enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv554347	chr11:49111467-49862647	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1044070	chr11:49147743-49448774	Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv525454	chr11:49156039-49570587	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11040261	SLC35C1	cis	cerebellum	SCAN
rs11040261	OR4C3	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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