Variant report

Variant	rs4889176
Chromosome Location	chr16:80664271-80664272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:80663419..80665671-chr16:80688492..80690813,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13333767	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs2123279	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2123280	0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs2123281	0.84[AMR][1000 genomes]
rs4325579	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4586445	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4888102	0.84[AMR][1000 genomes]
rs4888103	0.84[AMR][1000 genomes]
rs4889167	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4889168	1.00[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4889170	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4889171	0.83[MEX][hapmap]
rs4889172	0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs4889173	0.90[GIH][hapmap];0.90[TSI][hapmap]
rs4889177	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4889178	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4889179	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4889180	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]
rs4889181	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56713233	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57872556	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59946023	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60236050	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60596417	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60992426	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66713144	0.82[ASN][1000 genomes]
rs74028350	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74028368	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8059592	1.00[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9922043	0.90[EUR][1000 genomes]
rs9924170	0.88[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	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	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4889176	GAN	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80630600-80668000	Weak transcription	Fetal Kidney	kidney
2	chr16:80640800-80669200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr16:80642200-80668200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr16:80644200-80666200	Weak transcription	Brain Substantia Nigra	brain
5	chr16:80646600-80687800	Weak transcription	Pancreas	Pancrea
6	chr16:80647000-80665000	Weak transcription	Gastric	stomach
7	chr16:80653200-80668200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr16:80653600-80666800	Weak transcription	Esophagus	oesophagus
9	chr16:80653600-80667400	Weak transcription	Fetal Stomach	stomach
10	chr16:80654400-80667800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr16:80654400-80668800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr16:80657200-80668000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr16:80658000-80667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr16:80658000-80668200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr16:80658400-80666600	Weak transcription	HUVEC	blood vessel
16	chr16:80658800-80668200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr16:80660000-80668800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr16:80660200-80666800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr16:80661400-80667600	Strong transcription	Hela-S3	cervix
20	chr16:80661600-80666800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr16:80662200-80669000	Weak transcription	Brain Hippocampus Middle	brain
22	chr16:80662400-80665600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr16:80662400-80668600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr16:80662600-80665000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr16:80662600-80665000	Strong transcription	Fetal Intestine Small	intestine
26	chr16:80662600-80666600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:80662800-80665800	Weak transcription	Adipose Nuclei	Adipose
28	chr16:80663000-80668400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr16:80663000-80669200	Weak transcription	Liver	Liver
30	chr16:80663200-80665200	Weak transcription	Aorta	Aorta
31	chr16:80663200-80666600	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr16:80663200-80667200	Strong transcription	Placenta	Placenta
33	chr16:80663200-80668600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr16:80663200-80690200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr16:80663400-80666600	Weak transcription	Lung	lung
36	chr16:80663400-80666600	Weak transcription	Spleen	Spleen
37	chr16:80663400-80668800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr16:80663600-80665000	Strong transcription	Primary hematopoietic stem cells	blood
39	chr16:80663800-80665200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr16:80664200-80675800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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