Variant report

Variant	rs709421
Chromosome Location	chr16:12281317-12281318
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12270577..12272418-chr16:12280264..12282232,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11642667	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1701111	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1704094	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1704130	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2456272	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2968353	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs709418	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs709419	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs709420	0.99[ASN][1000 genomes]
rs709422	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8062913	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs830696	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830698	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830700	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830701	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs830704	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs830705	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830706	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs830707	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830708	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs830709	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830710	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs830724	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs830725	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs844224	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs844225	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs853869	0.90[AMR][1000 genomes]
rs853870	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs862692	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs865533	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs866180	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs905952	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs937965	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9934120	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[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	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	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:58 , 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	chr16:12257000-12296800	Weak transcription	Thymus	Thymus
3	chr16:12261200-12293400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr16:12261200-12293600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr16:12261400-12292400	Weak transcription	GM12878-XiMat	blood
6	chr16:12261800-12322000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:12262600-12282200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr16:12263200-12287600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr16:12271400-12293600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr16:12272200-12282200	Weak transcription	Right Atrium	heart
11	chr16:12272400-12281800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr16:12272400-12282600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr16:12272400-12282600	Weak transcription	Ovary	ovary
14	chr16:12272600-12282400	Weak transcription	Aorta	Aorta
15	chr16:12272800-12281600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr16:12276600-12281600	Weak transcription	Brain Germinal Matrix	brain
17	chr16:12276800-12296800	Weak transcription	Gastric	stomach
18	chr16:12277600-12286400	Strong transcription	Primary B cells from cord blood	blood
19	chr16:12278000-12284600	Enhancers	HSMMtube	muscle
20	chr16:12278200-12281800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr16:12278600-12283000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr16:12278600-12299400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:12278800-12282600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr16:12279000-12282400	Weak transcription	Psoas Muscle	Psoas
25	chr16:12279000-12283600	Enhancers	Esophagus	oesophagus
26	chr16:12279200-12282200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr16:12279800-12281600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr16:12279800-12281800	Weak transcription	Placenta	Placenta
29	chr16:12279800-12282000	Weak transcription	Brain Anterior Caudate	brain
30	chr16:12279800-12282200	Weak transcription	Brain Hippocampus Middle	brain
31	chr16:12279800-12282200	Weak transcription	Brain Substantia Nigra	brain
32	chr16:12279800-12283200	Weak transcription	Primary T cells from cord blood	blood
33	chr16:12279800-12284000	Weak transcription	Spleen	Spleen
34	chr16:12279800-12297800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr16:12280200-12282400	Enhancers	Liver	Liver
36	chr16:12280200-12282800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr16:12280200-12283200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr16:12280200-12283200	Enhancers	HepG2	liver
39	chr16:12280200-12283400	Enhancers	HSMM	muscle
40	chr16:12280400-12282400	Enhancers	NHEK	skin
41	chr16:12280400-12283000	Enhancers	Left Ventricle	heart
42	chr16:12280400-12283200	Enhancers	NHDF-Ad	bronchial
43	chr16:12280600-12282000	Weak transcription	Fetal Heart	heart
44	chr16:12280600-12282200	Weak transcription	Fetal Muscle Leg	muscle
45	chr16:12280800-12281600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr16:12280800-12281600	Weak transcription	Small Intestine	intestine
47	chr16:12280800-12282400	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr16:12280800-12283000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr16:12281000-12281400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr16:12281000-12281400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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