Variant report

Variant	rs8057859
Chromosome Location	chr16:80659234-80659235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:80658450..80660494-chr16:80660496..80663091,2	MCF-7	breast:
2	chr16:80653589..80657400-chr16:80657593..80661612,3	K562	blood:
3	chr16:80657007..80659717-chr16:80664386..80666332,2	K562	blood:
4	chr16:80654014..80661253-chr16:80836600..80840694,9	MCF-7	breast:
5	chr16:80657950..80660118-chr16:80836861..80838846,2	MCF-7	breast:
6	chr16:80653485..80655242-chr16:80656903..80659850,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260064	Chromatin interaction
ENSG00000166446	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1109546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1109547	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1121651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12448290	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13329877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13333767	0.94[ASW][hapmap];0.90[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13333789	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13335153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13338587	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2123279	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2123280	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4888100	0.93[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes]
rs4888101	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes]
rs4888102	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4889166	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes]
rs4889167	0.88[JPT][hapmap]
rs4889168	0.86[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs4889169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889170	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4889171	0.95[JPT][hapmap]
rs4889172	0.95[JPT][hapmap]
rs57013064	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs58873968	0.93[AFR][1000 genomes]
rs59675671	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59946023	0.88[ASN][1000 genomes]
rs66713144	0.80[EUR][1000 genomes]
rs9924170	0.99[ASN][1000 genomes]
rs9927571	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9932109	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1056083	chr16:80636184-80666779	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1063971	chr16:80640278-80663092	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1063761	chr16:80640278-80663665	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8057859	GAN	cis	cerebellum	SCAN
rs8057859	GABARAPL2	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80630600-80668000	Weak transcription	Fetal Kidney	kidney
2	chr16:80634200-80663600	Weak transcription	Brain Anterior Caudate	brain
3	chr16:80640600-80662200	Weak transcription	Primary T cells from cord blood	blood
4	chr16:80640600-80662600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr16:80640800-80663800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr16:80640800-80669200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr16:80642200-80668200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr16:80642800-80663800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr16:80644200-80666200	Weak transcription	Brain Substantia Nigra	brain
10	chr16:80646400-80662200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr16:80646400-80662200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr16:80646600-80687800	Weak transcription	Pancreas	Pancrea
13	chr16:80647000-80665000	Weak transcription	Gastric	stomach
14	chr16:80650000-80661800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr16:80650400-80659800	Strong transcription	Hela-S3	cervix
16	chr16:80653200-80668200	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr16:80653600-80662200	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr16:80653600-80666800	Weak transcription	Esophagus	oesophagus
19	chr16:80653600-80667400	Weak transcription	Fetal Stomach	stomach
20	chr16:80653800-80662000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr16:80654400-80662000	Weak transcription	Liver	Liver
22	chr16:80654400-80667800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr16:80654400-80668800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr16:80654800-80662200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr16:80655000-80661800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr16:80655000-80662400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr16:80657200-80668000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr16:80658000-80661600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr16:80658000-80667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr16:80658000-80668200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr16:80658200-80661800	Weak transcription	Aorta	Aorta
32	chr16:80658200-80662000	Weak transcription	Spleen	Spleen
33	chr16:80658400-80666600	Weak transcription	HUVEC	blood vessel
34	chr16:80658800-80659600	Enhancers	Placenta	Placenta
35	chr16:80658800-80668200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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