Variant report

Variant	rs3808776
Chromosome Location	chr9:17590299-17590300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BNC2-5	chr9:17589159-17590751	NONHSAT130305

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10113874	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10116876	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10120378	0.87[ASN][1000 genomes]
rs1022718	0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1028594	0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10435770	0.84[ASN][1000 genomes]
rs10756891	0.88[ASN][1000 genomes]
rs10810811	0.91[ASN][1000 genomes]
rs10810812	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs13294100	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs2180905	0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[ASN][1000 genomes]
rs2383031	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3758216	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs3758217	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs3780254	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs3808772	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3808775	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs4590535	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4961575	0.86[ASW][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7028060	0.89[ASN][1000 genomes]
rs7029346	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7030014	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7047611	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7047709	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7849043	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7859530	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7867956	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.99[ASN][1000 genomes]
rs8181077	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv892671	chr9:17378776-17610211	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv2422265	chr9:17396711-17598187	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv517380	chr9:17564267-17633232	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv466274	chr9:17564267-17633232	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv613701	chr9:17564267-17633232	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv892672	chr9:17564267-17634566	Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1025072	chr9:17577141-17632543	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1030902	chr9:17581039-17633296	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv13454	chr9:17581146-17634284	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1019764	chr9:17581410-17635571	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv2764160	chr9:17581422-17636674	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1033807	chr9:17581553-17633296	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv613702	chr9:17583310-17630591	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv466275	chr9:17583310-17631552	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv466276	chr9:17583310-17631552	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv613703	chr9:17583310-17631552	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv466277	chr9:17583310-17633232	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv466278	chr9:17583310-17633232	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv613704	chr9:17583310-17633232	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv1029253	chr9:17585687-17632543	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv1032604	chr9:17585687-17633296	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv1021448	chr9:17585687-17634920	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv1022691	chr9:17585687-17636337	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv1017917	chr9:17590299-17632364	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
28	nsv1024129	chr9:17590299-17632543	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
29	nsv1015810	chr9:17590299-17633296	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
30	nsv1031193	chr9:17590299-17636674	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17590000-17590600	Enhancers	Pancreatic Islets	Pancreatic Islet

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