Variant report

Variant	rs16960700
Chromosome Location	chr17:20029225-20029226
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20026531..20029286-chr17:20029731..20031735,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212186	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11868429	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12051844	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12051865	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16960715	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16960717	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16960730	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16960735	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1971043	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1971044	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751979	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3764436	0.94[ASN][1000 genomes]
rs57110692	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61141789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61660810	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587060	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587061	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587218	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587221	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7207458	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7211948	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7213349	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7213816	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7215097	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7215432	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7218859	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73299658	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73301548	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73309111	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73981849	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8076627	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8077051	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8077852	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9896190	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9897161	0.92[ASN][1000 genomes]
rs9897168	0.92[ASN][1000 genomes]
rs9899514	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9901102	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9902683	0.94[ASN][1000 genomes]
rs9905976	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9908032	0.81[ASN][1000 genomes]
rs9911605	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9913018	0.85[ASN][1000 genomes]
rs9913394	0.89[EUR][1000 genomes]
rs9914219	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9941362	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9941376	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16960700	AKAP10	cis	Whole Blood	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19999000-20032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr17:20002200-20033400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr17:20025400-20040400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:20025600-20031000	Weak transcription	Left Ventricle	heart
5	chr17:20025600-20034600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr17:20025800-20029800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:20025800-20030200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr17:20025800-20031000	Weak transcription	Hela-S3	cervix
9	chr17:20025800-20037600	Weak transcription	Ovary	ovary
10	chr17:20025800-20044400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:20026000-20031000	Weak transcription	Fetal Brain Female	brain
12	chr17:20026000-20031400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr17:20026200-20040000	Weak transcription	Aorta	Aorta
14	chr17:20026200-20049800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr17:20026600-20031200	Weak transcription	Fetal Brain Male	brain
16	chr17:20026600-20033200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr17:20027000-20031000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr17:20028600-20029400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:20028600-20029600	Genic enhancers	Brain Cingulate Gyrus	brain
20	chr17:20028600-20029800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr17:20028600-20030200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr17:20028800-20029400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr17:20028800-20029400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr17:20028800-20029400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr17:20028800-20029400	Enhancers	NHLF	lung
26	chr17:20028800-20029600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr17:20028800-20029600	Enhancers	Adipose Nuclei	Adipose
28	chr17:20028800-20030000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr17:20028800-20030000	Enhancers	Brain Substantia Nigra	brain
30	chr17:20028800-20030200	Enhancers	Brain Anterior Caudate	brain
31	chr17:20028800-20031600	Enhancers	Brain Angular Gyrus	brain
32	chr17:20029000-20029600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr17:20029000-20030000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr17:20029000-20030200	Enhancers	Brain Hippocampus Middle	brain
35	chr17:20029200-20029400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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