Variant report

Variant	rs11639640
Chromosome Location	chr16:12356540-12356541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11075057	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11075058	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11075059	0.86[EUR][1000 genomes]
rs11644788	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11649626	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861914	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12148953	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12445263	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12445569	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12446650	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12448443	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13335852	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17697005	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17764604	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2089251	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs209851	0.81[EUR][1000 genomes]
rs209856	0.83[EUR][1000 genomes]
rs2856771	0.83[EUR][1000 genomes]
rs2904423	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35818743	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4305040	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4780417	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4780418	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4780419	0.88[EUR][1000 genomes]
rs4781200	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4781201	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4781202	0.91[EUR][1000 genomes]
rs544598	0.80[EUR][1000 genomes]
rs6498274	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7189386	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7189945	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7191442	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7192102	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7194718	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7194981	0.88[EUR][1000 genomes]
rs7195520	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7197417	0.92[EUR][1000 genomes]
rs7199556	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7200289	0.86[EUR][1000 genomes]
rs7204209	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7204333	0.86[EUR][1000 genomes]
rs7500910	0.84[EUR][1000 genomes]
rs8046012	0.87[EUR][1000 genomes]
rs8051758	0.86[EUR][1000 genomes]
rs8058876	0.82[ASN][1000 genomes]
rs8061549	0.91[EUR][1000 genomes]
rs8063991	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs868773	0.85[GIH][hapmap];0.87[EUR][1000 genomes]
rs869289	0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs905950	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630612	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9921728	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9927705	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9928214	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9930625	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9937220	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv905348	chr16:12299936-12358206	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3406779	chr16:12356462-12356647	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12308000-12371400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr16:12309800-12371200	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr16:12323400-12394200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr16:12323800-12373000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr16:12330800-12373000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr16:12334000-12356600	Weak transcription	Right Atrium	heart
7	chr16:12334600-12371800	Weak transcription	Adipose Nuclei	Adipose
8	chr16:12338200-12396200	Weak transcription	Thymus	Thymus
9	chr16:12347800-12395200	Weak transcription	Right Ventricle	heart
10	chr16:12348200-12371400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr16:12350200-12371600	Weak transcription	GM12878-XiMat	blood
12	chr16:12351200-12373000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:12351200-12382800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:12353200-12358200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr16:12353400-12356600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr16:12353800-12356600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr16:12353800-12356600	Weak transcription	Brain Angular Gyrus	brain
18	chr16:12354400-12357000	Flanking Active TSS	HepG2	liver
19	chr16:12354600-12358000	Weak transcription	Lung	lung
20	chr16:12354600-12358800	Weak transcription	Fetal Heart	heart
21	chr16:12354800-12356600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr16:12354800-12361400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr16:12354800-12382800	Weak transcription	Gastric	stomach
24	chr16:12355000-12361000	Weak transcription	Placenta	Placenta
25	chr16:12355000-12361200	Weak transcription	Ovary	ovary
26	chr16:12355000-12366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr16:12355200-12372000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr16:12355800-12357000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr16:12355800-12357000	Enhancers	Pancreas	Pancrea
30	chr16:12355800-12357200	Enhancers	Esophagus	oesophagus
31	chr16:12356000-12356800	Enhancers	Fetal Intestine Large	intestine
32	chr16:12356000-12356800	Enhancers	Fetal Kidney	kidney
33	chr16:12356000-12356800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr16:12356000-12356800	Enhancers	Fetal Lung	lung
35	chr16:12356000-12357400	Enhancers	A549	lung
36	chr16:12356000-12360400	Strong transcription	Primary T cells from cord blood	blood
37	chr16:12356000-12361800	Enhancers	Fetal Muscle Leg	muscle
38	chr16:12356000-12390200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr16:12356200-12356600	Flanking Active TSS	Liver	Liver
40	chr16:12356200-12356600	Enhancers	Small Intestine	intestine
41	chr16:12356200-12356800	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr16:12356200-12356800	Enhancers	Brain Hippocampus Middle	brain
43	chr16:12356200-12356800	Enhancers	Duodenum Mucosa	Duodenum
44	chr16:12356200-12356800	Enhancers	Fetal Intestine Small	intestine
45	chr16:12356200-12356800	Enhancers	Left Ventricle	heart
46	chr16:12356200-12357000	Enhancers	Brain Cingulate Gyrus	brain
47	chr16:12356200-12357000	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr16:12356200-12357000	Enhancers	Stomach Smooth Muscle	stomach
49	chr16:12356200-12357400	Enhancers	Brain Germinal Matrix	brain
50	chr16:12356200-12357400	Enhancers	Rectal Mucosa Donor 31	rectum

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