Variant report

Variant	rs12447921
Chromosome Location	chr16:80717459-80717460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:80715724..80718304-chr16:80740756..80743210,2	MCF-7	breast:
2	chr16:80715158..80718129-chr16:80746227..80748561,2	MCF-7	breast:
3	chr16:80711707..80713516-chr16:80717289..80718938,2	MCF-7	breast:
4	chr16:80709777..80712753-chr16:80715785..80718151,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1026247	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10514505	0.89[AMR][1000 genomes]
rs10514506	0.95[MEX][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10747208	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1077885	0.81[CEU][hapmap];0.87[AMR][1000 genomes]
rs1077886	0.84[CEU][hapmap];0.91[AMR][1000 genomes]
rs10871392	0.90[AMR][1000 genomes]
rs10871393	0.91[AMR][1000 genomes]
rs10871394	0.89[AMR][1000 genomes]
rs11150298	0.81[CEU][hapmap]
rs11150299	0.81[CEU][hapmap];0.87[AMR][1000 genomes]
rs11150300	0.93[ASW][hapmap];0.84[CEU][hapmap];0.95[MEX][hapmap];0.90[AMR][1000 genomes]
rs11150301	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11150302	0.88[AMR][1000 genomes]
rs11643733	0.92[CEU][hapmap];0.89[AMR][1000 genomes]
rs11859496	0.81[AMR][1000 genomes]
rs11863297	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs16953809	0.86[AMR][1000 genomes]
rs2012766	0.81[CEU][hapmap]
rs2084866	0.81[CEU][hapmap];0.89[AMR][1000 genomes]
rs2316148	0.89[AMR][1000 genomes]
rs2316152	0.80[AMR][1000 genomes]
rs2873084	0.85[CEU][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs35732345	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55653646	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56032204	0.90[AMR][1000 genomes]
rs6564778	0.82[CEU][hapmap]
rs6564779	0.85[CEU][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7187646	0.87[MEX][hapmap];0.83[AMR][1000 genomes]
rs7190973	0.83[AMR][1000 genomes]
rs7192094	0.88[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7193379	0.84[YRI][hapmap]
rs7195952	0.81[AMR][1000 genomes]
rs7200113	0.81[AMR][1000 genomes]
rs8047798	0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs8047972	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8047993	0.81[CEU][hapmap]
rs8048068	0.92[CEU][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8049284	0.82[MEX][hapmap]
rs8052730	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8057515	0.81[CEU][hapmap];0.86[AMR][1000 genomes]
rs896627	0.91[AMR][1000 genomes]
rs896628	0.81[CEU][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes]
rs896629	0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs930743	0.81[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs930744	0.85[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060621	chr16:80532848-80980616	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv542989	chr16:80532848-80980616	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1057357	chr16:80662770-80794945	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3451298	chr16:80696935-80997389	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3350075	chr16:80696955-80997359	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	esv1815070	chr16:80697870-80725811	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv33408	chr16:80706129-80745371	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12447921	ADAT1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:80689000-80751000	Weak transcription	Pancreas	Pancrea
2	chr16:80690600-80728000	Weak transcription	Gastric	stomach
3	chr16:80699400-80723000	Weak transcription	HUVEC	blood vessel
4	chr16:80701600-80717800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr16:80703400-80723400	Weak transcription	Esophagus	oesophagus
6	chr16:80704600-80721000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr16:80706200-80734400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr16:80710400-80718000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr16:80710400-80718400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr16:80710400-80723200	Weak transcription	Brain Anterior Caudate	brain
11	chr16:80710800-80723400	Weak transcription	Adipose Nuclei	Adipose
12	chr16:80711400-80717800	Weak transcription	Spleen	Spleen
13	chr16:80713200-80718200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr16:80714400-80718000	Weak transcription	Lung	lung
15	chr16:80714800-80719000	Strong transcription	Fetal Intestine Small	intestine
16	chr16:80715000-80719800	Weak transcription	Fetal Intestine Large	intestine
17	chr16:80715400-80721800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr16:80715800-80718200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr16:80715800-80720400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr16:80716000-80720000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr16:80716000-80723400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr16:80716000-80724200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr16:80716400-80717600	Enhancers	NHLF	lung
24	chr16:80716400-80720200	Weak transcription	Fetal Stomach	stomach
25	chr16:80716600-80718400	Weak transcription	Aorta	Aorta
26	chr16:80716600-80718600	Weak transcription	Liver	Liver
27	chr16:80716600-80720000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr16:80716800-80717800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr16:80716800-80719000	Weak transcription	Fetal Muscle Leg	muscle
30	chr16:80716800-80719200	Strong transcription	Hela-S3	cervix
31	chr16:80717000-80717600	Enhancers	Brain Angular Gyrus	brain
32	chr16:80717000-80720200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr16:80717200-80719800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr16:80717200-80724800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr16:80717400-80717600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr16:80717400-80718000	Weak transcription	Placenta	Placenta
37	chr16:80717400-80724600	Weak transcription	Muscle Satellite Cultured Cells	--

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