Variant report

Variant	rs7871351
Chromosome Location	chr9:17630427-17630428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTLN-5	chr9:17630352-17630427	NONHSAT130304

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12238302	0.83[AFR][1000 genomes]
rs1998247	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1998248	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3808731	0.81[ASN][1000 genomes]
rs3808734	0.84[CEU][hapmap]

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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	esv2752287	chr9:17593258-17632543	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
30	nsv1015153	chr9:17596833-17632364	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17626400-17633200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:17627600-17630600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:17628400-17631200	Weak transcription	NH-A	brain
4	chr9:17628600-17630600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:17629400-17631000	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr9:17629800-17631200	Weak transcription	Liver	Liver
7	chr9:17630000-17633200	Weak transcription	Fetal Brain Male	brain
8	chr9:17630400-17630800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:17630400-17630800	Flanking Active TSS	Hela-S3	cervix
10	chr9:17630400-17631000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr9:17630400-17631200	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links