Variant report

Variant	rs12445236
Chromosome Location	chr16:12299936-12299937
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	chr16:12299412..12301084-chr16:12329409..12330964,2	K562	blood:
4	chr16:12298925..12300602-chr16:12300728..12302688,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11642364	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11642867	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11643843	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11644280	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11644612	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11646544	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11647545	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11647857	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12444353	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12446101	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12447822	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1472979	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1809989	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3844114	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4781189	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4781190	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4781191	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4781192	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4781194	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4781195	0.98[ASN][1000 genomes]
rs4781196	0.99[ASN][1000 genomes]
rs55939888	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6498269	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6498270	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67401564	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192589	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7193992	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7193997	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7197299	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7206824	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73504103	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73521875	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8046606	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs830717	0.84[CHB][hapmap]
rs9788826	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788917	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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	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
4	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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12261800-12322000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr16:12282800-12305400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr16:12282800-12322600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr16:12283200-12300200	Weak transcription	NHEK	skin
5	chr16:12283200-12302000	Weak transcription	NHDF-Ad	bronchial
6	chr16:12283400-12310200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:12287800-12302200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr16:12291400-12316200	Strong transcription	Primary T cells from cord blood	blood
9	chr16:12292200-12322200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr16:12292600-12300400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr16:12292600-12301400	Weak transcription	GM12878-XiMat	blood
12	chr16:12292800-12310200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr16:12293000-12302400	Strong transcription	Primary B cells from cord blood	blood
14	chr16:12293200-12300200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:12293600-12319800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr16:12294800-12322400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr16:12295200-12311400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr16:12295600-12319800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr16:12295800-12320800	Weak transcription	HSMMtube	muscle
20	chr16:12296200-12319800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr16:12296600-12322600	Weak transcription	Right Ventricle	heart
22	chr16:12296800-12313000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr16:12297000-12301400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr16:12297000-12301800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr16:12297000-12322400	Weak transcription	Ovary	ovary
26	chr16:12297200-12305000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr16:12297200-12305800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr16:12297200-12309600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr16:12297400-12353800	Weak transcription	Gastric	stomach
30	chr16:12297600-12300600	Enhancers	Fetal Stomach	stomach
31	chr16:12297800-12310600	Weak transcription	Thymus	Thymus
32	chr16:12298000-12310600	Weak transcription	Pancreas	Pancrea
33	chr16:12298200-12300400	Enhancers	HepG2	liver
34	chr16:12298200-12302000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr16:12298400-12307800	Weak transcription	Brain Substantia Nigra	brain
36	chr16:12298400-12319400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr16:12298600-12307800	Weak transcription	Brain Angular Gyrus	brain
38	chr16:12298800-12322000	Weak transcription	Fetal Muscle Leg	muscle
39	chr16:12299000-12302200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr16:12299200-12307400	Weak transcription	Brain Hippocampus Middle	brain
41	chr16:12299400-12300400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr16:12299400-12303600	Enhancers	Placenta	Placenta
43	chr16:12299400-12308200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr16:12299600-12300800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr16:12299600-12301200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr16:12299600-12301800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr16:12299600-12302000	Weak transcription	Esophagus	oesophagus
48	chr16:12299600-12309000	Weak transcription	Aorta	Aorta
49	chr16:12299600-12322200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr16:12299600-12322400	Weak transcription	Spleen	Spleen

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