Variant report

Variant	rs11643843
Chromosome Location	chr16:12250819-12250820
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11642364	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11642867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11644280	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11644612	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11646544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11647545	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11647857	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12444353	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12445236	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12446101	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12447822	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1472979	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1809989	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3844114	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4781189	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4781190	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4781191	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4781192	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4781194	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4781195	0.93[ASN][1000 genomes]
rs4781196	0.93[ASN][1000 genomes]
rs55939888	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6498269	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6498270	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67401564	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7192589	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7193992	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7193997	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7197299	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206824	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73504103	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73521875	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8046606	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs830717	0.84[CHB][hapmap]
rs9788826	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9788917	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[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	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	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1042146	chr16:12208242-12256699	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1039590	chr16:12237623-12279574	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12213800-12255400	Weak transcription	Gastric	stomach
2	chr16:12229800-12251400	Weak transcription	NHEK	skin
3	chr16:12229800-12253600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr16:12230200-12256200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr16:12231400-12251000	Weak transcription	Ovary	ovary
6	chr16:12231400-12268000	Weak transcription	Pancreas	Pancrea
7	chr16:12233600-12251000	Weak transcription	NHDF-Ad	bronchial
8	chr16:12234600-12261600	Weak transcription	Aorta	Aorta
9	chr16:12234600-12265600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr16:12235400-12251000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr16:12242200-12251000	Weak transcription	HSMMtube	muscle
12	chr16:12242200-12252400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr16:12242200-12252400	Weak transcription	Left Ventricle	heart
14	chr16:12242200-12252600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr16:12242200-12252600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr16:12242200-12253800	Weak transcription	Right Atrium	heart
17	chr16:12242200-12255200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr16:12242200-12261600	Weak transcription	Lung	lung
19	chr16:12242200-12262800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr16:12242200-12299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr16:12242400-12252400	Weak transcription	Right Ventricle	heart
22	chr16:12242400-12252600	Weak transcription	Fetal Brain Female	brain
23	chr16:12242400-12252800	Weak transcription	Brain Anterior Caudate	brain
24	chr16:12242400-12255800	Weak transcription	Thymus	Thymus
25	chr16:12242400-12256400	Weak transcription	Fetal Kidney	kidney
26	chr16:12242400-12264600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr16:12242400-12280600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr16:12243200-12255400	Weak transcription	Psoas Muscle	Psoas
29	chr16:12244000-12251200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr16:12244000-12252800	Weak transcription	Fetal Muscle Leg	muscle
31	chr16:12244400-12255800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr16:12244800-12261200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr16:12245600-12251600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr16:12245600-12257200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr16:12245600-12261800	Weak transcription	Fetal Thymus	thymus
36	chr16:12246600-12252400	Weak transcription	Brain Hippocampus Middle	brain
37	chr16:12247000-12252400	Weak transcription	Brain Substantia Nigra	brain
38	chr16:12247400-12259400	Strong transcription	Primary B cells from cord blood	blood
39	chr16:12248000-12258400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr16:12248200-12255200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr16:12248400-12251000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr16:12248800-12254000	Strong transcription	Adipose Nuclei	Adipose
43	chr16:12248800-12257800	Strong transcription	Primary T cells from cord blood	blood
44	chr16:12249400-12251000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr16:12249600-12251000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr16:12249600-12254000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr16:12249600-12256400	Weak transcription	HepG2	liver
48	chr16:12249800-12252200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr16:12250000-12251000	Weak transcription	Esophagus	oesophagus
50	chr16:12250000-12257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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