Variant report

Variant	rs4887833
Chromosome Location	chr16:75614272-75614273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75613643..75617035-chr16:75620700..75623039,3	MCF-7	breast:
2	chr16:75593250..75596560-chr16:75613588..75617138,3	MCF-7	breast:
3	chr16:75613514..75616148-chr16:75621638..75623239,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GABARAPL2-3	chr16:75613803-75615450	NONHSAT143748
2	lnc-GABARAPL2-3	chr16:75614134-75614559	NONHSAT143749

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11149842	0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12445389	0.81[AMR][1000 genomes]
rs12445937	0.81[AMR][1000 genomes]
rs12446652	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12595883	0.84[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.87[AMR][1000 genomes]
rs12596033	0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs12596724	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12596857	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12598094	0.80[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12598741	0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12598751	0.81[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes]
rs12599212	0.87[AMR][1000 genomes]
rs12599322	0.88[JPT][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12600066	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12600271	0.94[JPT][hapmap];0.91[AMR][1000 genomes]
rs16940253	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16940467	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16941533	0.80[ASN][1000 genomes]
rs17697211	0.86[AMR][1000 genomes]
rs17764821	0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs1812507	0.87[AMR][1000 genomes]
rs1836547	0.83[AMR][1000 genomes]
rs1865493	0.86[JPT][hapmap]
rs1979717	0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2082751	0.81[ASN][1000 genomes]
rs2164245	0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2242406	0.81[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs2278469	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2289063	0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs2903106	0.83[ASN][1000 genomes]
rs3736377	0.96[MEX][hapmap];0.82[AMR][1000 genomes]
rs3743599	0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs3743601	0.87[AMR][1000 genomes]
rs3743603	0.80[CHD][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3743605	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3784929	0.90[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap]
rs3851741	1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs41505349	0.97[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs4888436	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4888437	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4888440	0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs4888442	0.86[AMR][1000 genomes]
rs5010692	0.97[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs57252551	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57396453	0.81[ASN][1000 genomes]
rs58273293	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58508930	0.85[AMR][1000 genomes]
rs58597869	0.90[AMR][1000 genomes]
rs58673511	0.82[AMR][1000 genomes]
rs58719566	0.91[AMR][1000 genomes]
rs59907199	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60393074	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60952428	0.82[AMR][1000 genomes]
rs61036571	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61078946	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61539645	0.80[AMR][1000 genomes]
rs6564268	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7186966	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7187672	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7193066	0.83[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs7195338	0.85[AMR][1000 genomes]
rs719574	0.84[AMR][1000 genomes]
rs7206799	0.87[AMR][1000 genomes]
rs73615030	0.87[ASN][1000 genomes]
rs74027438	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7499759	0.90[AMR][1000 genomes]
rs8051241	0.92[ASN][1000 genomes]
rs8051713	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8053219	0.91[MEX][hapmap]
rs8056968	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8060972	0.82[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8061505	0.81[ASN][1000 genomes]
rs8192516	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs963820	1.00[CEU][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9788802	0.85[AMR][1000 genomes]
rs9934159	0.82[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
5	nsv532561	chr16:75519574-75636977	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75601200-75624400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:75601600-75614400	Genic enhancers	Brain Anterior Caudate	brain
3	chr16:75601600-75615200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr16:75601600-75615400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr16:75601800-75614400	Strong transcription	Thymus	Thymus
6	chr16:75601800-75615400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr16:75602000-75614400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr16:75602000-75614600	Strong transcription	Placenta	Placenta
9	chr16:75602000-75615000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr16:75602000-75615200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr16:75602200-75614400	Strong transcription	Fetal Intestine Large	intestine
12	chr16:75602200-75614800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr16:75602600-75614400	Strong transcription	Fetal Brain Female	brain
14	chr16:75602800-75614400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr16:75602800-75615400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr16:75603000-75614800	Strong transcription	Primary T cells from cord blood	blood
17	chr16:75603400-75614400	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr16:75603400-75614600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr16:75603400-75615000	Strong transcription	Dnd41	blood
20	chr16:75604000-75615400	Strong transcription	Fetal Stomach	stomach
21	chr16:75604200-75614400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr16:75604200-75622600	Weak transcription	Right Atrium	heart
23	chr16:75604400-75614600	Strong transcription	Fetal Muscle Leg	muscle
24	chr16:75605400-75615400	Strong transcription	Fetal Thymus	thymus
25	chr16:75605400-75616000	Strong transcription	Fetal Intestine Small	intestine
26	chr16:75606400-75615200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr16:75607000-75614400	Strong transcription	Liver	Liver
28	chr16:75607000-75623200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr16:75607200-75615200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr16:75607400-75614400	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr16:75607400-75614600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr16:75607600-75614400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr16:75607600-75614400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr16:75607600-75615800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr16:75607600-75630800	Weak transcription	Fetal Brain Male	brain
36	chr16:75607800-75614400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr16:75607800-75614800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr16:75608000-75614400	Strong transcription	Rectal Smooth Muscle	rectum
39	chr16:75608400-75614600	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr16:75608800-75614600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr16:75608800-75616600	Weak transcription	Stomach Mucosa	stomach
42	chr16:75609000-75627800	Weak transcription	NHEK	skin
43	chr16:75610000-75615400	Strong transcription	Aorta	Aorta
44	chr16:75610200-75615000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr16:75610400-75634000	Weak transcription	Hela-S3	cervix
46	chr16:75610600-75614400	Strong transcription	Brain Hippocampus Middle	brain
47	chr16:75610600-75614400	Strong transcription	Left Ventricle	heart
48	chr16:75610600-75622800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr16:75610600-75622800	Weak transcription	Fetal Heart	heart
50	chr16:75610600-75633400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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