Variant report

Variant	rs2208496
Chromosome Location	chr9:17633232-17633233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12349497	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1998246	0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs2208498	0.83[CHB][hapmap]
rs2224448	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2224450	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs3808737	0.92[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3808741	0.92[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4961580	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs4961581	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4961583	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6475158	0.91[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7039154	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9406680	0.91[CHB][hapmap];0.87[CHD][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9407825	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	nsv892674	chr9:17631186-17699981	Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2208496	SH3GL2	cis	parietal	SCAN
rs2208496	IFNA8	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17630800-17637800	Enhancers	Hela-S3	cervix
2	chr9:17631000-17633600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:17633200-17633400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:17633200-17633400	Enhancers	Fetal Brain Male	brain

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