Variant report

Variant	rs4889169
Chromosome Location	chr16:80654633-80654634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:80654063..80656286-chr16:80664938..80666580,2	MCF-7	breast:
2	chr16:80654095..80656173-chr16:80667578..80669313,2	MCF-7	breast:
3	chr16:80559928..80561785-chr16:80653051..80655923,2	MCF-7	breast:
4	chr16:80654459..80656206-chr16:80752582..80754185,2	MCF-7	breast:
5	chr16:80653224..80655610-chr16:80835327..80837663,2	MCF-7	breast:
6	chr16:80653589..80657400-chr16:80657593..80661612,3	K562	blood:
7	chr16:80654014..80661253-chr16:80836600..80840694,9	MCF-7	breast:
8	chr16:80653485..80655242-chr16:80656903..80659850,2	MCF-7	breast:
9	chr16:80653017..80657135-chr16:80751314..80754331,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166446	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1109546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109547	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1121651	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12448290	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13329877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13333767	0.90[CEU][hapmap];0.95[GIH][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs13333789	0.81[AMR][1000 genomes]
rs13335153	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13338587	0.80[AMR][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];0.90[EUR][1000 genomes]
rs4888101	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.98[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];0.92[EUR][1000 genomes]
rs4889167	0.88[JPT][hapmap]
rs4889168	0.86[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap]
rs4889170	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4889171	0.95[JPT][hapmap]
rs4889172	0.95[JPT][hapmap]
rs58873968	0.80[AMR][1000 genomes]
rs59675671	0.80[AMR][1000 genomes]
rs59946023	0.88[ASN][1000 genomes]
rs8057859	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]
rs9924170	1.00[ASN][1000 genomes]
rs9927571	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9932109	0.94[ASN][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4889169	GABARAPL2	cis	cerebellum	SCAN
rs4889169	GAN	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

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	chr16:80635400-80655600	Weak transcription	Brain Angular Gyrus	brain
4	chr16:80639800-80657400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr16:80640600-80662200	Weak transcription	Primary T cells from cord blood	blood
6	chr16:80640600-80662600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr16:80640800-80663800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr16:80640800-80669200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr16:80642200-80668200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr16:80642800-80663800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr16:80644200-80666200	Weak transcription	Brain Substantia Nigra	brain
12	chr16:80645400-80657600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:80646000-80656000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr16:80646400-80657800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr16:80646400-80662200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr16:80646400-80662200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr16:80646600-80654800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr16:80646600-80657800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr16:80646600-80687800	Weak transcription	Pancreas	Pancrea
20	chr16:80647000-80665000	Weak transcription	Gastric	stomach
21	chr16:80649600-80657800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr16:80649600-80658000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr16:80650000-80655200	Strong transcription	Fetal Intestine Small	intestine
24	chr16:80650000-80661800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr16:80650400-80659800	Strong transcription	Hela-S3	cervix
26	chr16:80650800-80656200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr16:80651400-80655400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr16:80651600-80654800	Weak transcription	Fetal Muscle Leg	muscle
29	chr16:80652200-80655000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr16:80652600-80654800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr16:80652600-80654800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr16:80652800-80657000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr16:80653000-80655800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr16:80653200-80668200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr16:80653400-80655000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr16:80653600-80657600	Weak transcription	Lung	lung
37	chr16:80653600-80658400	Enhancers	Placenta	Placenta
38	chr16:80653600-80662200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr16:80653600-80666800	Weak transcription	Esophagus	oesophagus
40	chr16:80653600-80667400	Weak transcription	Fetal Stomach	stomach
41	chr16:80653800-80657800	Weak transcription	Adipose Nuclei	Adipose
42	chr16:80653800-80662000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr16:80654000-80655600	Enhancers	Placenta Amnion	Placenta Amnion
44	chr16:80654000-80657800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr16:80654200-80656200	Weak transcription	Fetal Intestine Large	intestine
46	chr16:80654200-80657000	Weak transcription	HUVEC	blood vessel
47	chr16:80654200-80657600	Weak transcription	HSMMtube	muscle
48	chr16:80654200-80658400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr16:80654400-80657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr16:80654400-80657200	Weak transcription	Spleen	Spleen

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