Variant report

Variant	rs4889180
Chromosome Location	chr16:80671141-80671142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13333767	0.95[JPT][hapmap]
rs2123279	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs2123280	0.83[MEX][hapmap]
rs4325579	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4586445	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889167	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4889168	1.00[CEU][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs4889170	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4889172	0.83[MEX][hapmap]
rs4889173	0.92[GIH][hapmap];0.90[TSI][hapmap]
rs4889176	0.92[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4889177	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889178	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889179	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889181	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889183	0.80[EUR][1000 genomes]
rs56713233	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57872556	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59946023	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60236050	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60596417	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60992426	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66713144	0.87[ASN][1000 genomes]
rs74028350	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74028368	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8059592	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9922043	0.91[EUR][1000 genomes]
rs9924170	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060621	chr16:80532848-80980616	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv542989	chr16:80532848-80980616	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1055196	chr16:80647550-80672417	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1057562	chr16:80650768-80675842	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1058764	chr16:80656966-80707848	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1057357	chr16:80662770-80794945	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv275156	chr16:80666221-80672704	ZNF genes & repeats Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4889180	GAN	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80646600-80687800	Weak transcription	Pancreas	Pancrea
2	chr16:80663200-80690200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr16:80664200-80675800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr16:80665400-80677200	Weak transcription	Gastric	stomach
5	chr16:80667000-80671400	Weak transcription	HUVEC	blood vessel
6	chr16:80667200-80673000	Weak transcription	Placenta	Placenta
7	chr16:80667400-80675200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr16:80667400-80690000	Weak transcription	Spleen	Spleen
9	chr16:80667600-80672200	Weak transcription	Hela-S3	cervix
10	chr16:80667600-80673800	Weak transcription	Aorta	Aorta

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