Variant report

Variant	rs1472979
Chromosome Location	chr16:12299234-12299235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:12298053..12299977-chr16:12303938..12306592,2	MCF-7	breast:
2	chr16:12298240..12300602-chr16:12300728..12303474,2	K562	blood:
3	chr16:12292330..12294859-chr16:12296467..12299466,2	MCF-7	breast:
4	chr16:12298925..12300602-chr16:12300728..12302688,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11642364	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11642867	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11643843	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11644280	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11644612	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11646544	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11647545	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11647857	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12444353	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12445236	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12446101	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12447822	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1809989	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3844114	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4781189	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4781190	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4781191	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4781192	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4781194	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4781195	0.92[ASN][1000 genomes]
rs4781196	0.93[ASN][1000 genomes]
rs55939888	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6498269	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6498270	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67401564	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7192589	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7193992	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7193997	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7197299	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7206824	0.87[EUR][1000 genomes]
rs73504103	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73521875	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8046606	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs830717	0.84[CHB][hapmap]
rs9788826	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788917	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	nsv571461	chr16:12268830-12314451	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12242200-12299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr16:12261800-12322000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr16:12278600-12299400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:12282800-12305400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr16:12282800-12322600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr16:12283200-12300200	Weak transcription	NHEK	skin
7	chr16:12283200-12302000	Weak transcription	NHDF-Ad	bronchial
8	chr16:12283400-12310200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr16:12287800-12302200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr16:12291400-12316200	Strong transcription	Primary T cells from cord blood	blood
11	chr16:12292200-12322200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr16:12292600-12300400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr16:12292600-12301400	Weak transcription	GM12878-XiMat	blood
14	chr16:12292800-12310200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr16:12293000-12302400	Strong transcription	Primary B cells from cord blood	blood
16	chr16:12293200-12300200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr16:12293600-12319800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr16:12294200-12299800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr16:12294800-12322400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr16:12295200-12311400	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr16:12295600-12319800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr16:12295800-12320800	Weak transcription	HSMMtube	muscle
23	chr16:12296200-12319800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr16:12296400-12299600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr16:12296600-12299600	Genic enhancers	Spleen	Spleen
26	chr16:12296600-12322600	Weak transcription	Right Ventricle	heart
27	chr16:12296800-12313000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr16:12297000-12299400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr16:12297000-12301400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr16:12297000-12301800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr16:12297000-12322400	Weak transcription	Ovary	ovary
32	chr16:12297200-12299400	Weak transcription	Lung	lung
33	chr16:12297200-12305000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr16:12297200-12305800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr16:12297200-12309600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr16:12297400-12353800	Weak transcription	Gastric	stomach
37	chr16:12297600-12300600	Enhancers	Fetal Stomach	stomach
38	chr16:12297800-12310600	Weak transcription	Thymus	Thymus
39	chr16:12298000-12310600	Weak transcription	Pancreas	Pancrea
40	chr16:12298200-12299400	Weak transcription	Placenta	Placenta
41	chr16:12298200-12299600	Enhancers	Stomach Smooth Muscle	stomach
42	chr16:12298200-12300400	Enhancers	HepG2	liver
43	chr16:12298200-12302000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr16:12298400-12299600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr16:12298400-12307800	Weak transcription	Brain Substantia Nigra	brain
46	chr16:12298400-12319400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr16:12298600-12299600	Strong transcription	Aorta	Aorta
48	chr16:12298600-12299800	Strong transcription	Adipose Nuclei	Adipose
49	chr16:12298600-12307800	Weak transcription	Brain Angular Gyrus	brain
50	chr16:12298800-12299400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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