Variant report

Variant	rs6587221
Chromosome Location	chr17:20090069-20090070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20089910..20092717-chr17:20126449..20128094,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11868429	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12051550	0.86[ASN][1000 genomes]
rs12051844	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12051865	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16960700	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16960715	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960717	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960730	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16960735	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1971043	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1971044	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3751979	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57110692	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61141789	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61660810	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587060	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587061	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587218	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7207458	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7211948	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213349	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7213816	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7215097	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7215432	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7218859	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73299658	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73301548	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73309111	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73981849	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8076627	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8077051	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8077852	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9896190	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9899514	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9901102	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9901484	0.82[ASN][1000 genomes]
rs9905976	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9908032	0.82[ASN][1000 genomes]
rs9909156	0.86[ASN][1000 genomes]
rs9911605	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9913018	0.86[ASN][1000 genomes]
rs9913394	0.90[EUR][1000 genomes]
rs9914219	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9941362	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941376	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
6	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
7	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
8	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
9	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
10	nsv2003	chr17:20046306-20090653	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1057870	chr17:20079146-20121848	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv1063833	chr17:20088333-20206601	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers 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	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6587221	AKAP10	cis	Whole Blood	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20060800-20092200	Weak transcription	Fetal Intestine Small	intestine
2	chr17:20062000-20090400	Weak transcription	Aorta	Aorta
3	chr17:20075800-20090800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:20078600-20090400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr17:20080400-20092200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:20080400-20092400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:20082800-20092400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:20084200-20092000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr17:20084400-20092200	Weak transcription	Brain Germinal Matrix	brain
10	chr17:20085600-20093800	Enhancers	Brain Substantia Nigra	brain
11	chr17:20086000-20092200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr17:20086000-20092600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr17:20086600-20092000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr17:20087400-20092200	Enhancers	Brain Angular Gyrus	brain
15	chr17:20087600-20091400	Enhancers	Brain Anterior Caudate	brain
16	chr17:20087600-20091600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr17:20087600-20092200	Enhancers	Brain Cingulate Gyrus	brain
18	chr17:20087600-20092400	Enhancers	Brain Hippocampus Middle	brain
19	chr17:20087800-20091000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr17:20088400-20092000	Weak transcription	Fetal Brain Female	brain
21	chr17:20088600-20090600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr17:20088600-20092000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:20088600-20092000	Weak transcription	HMEC	breast
24	chr17:20088600-20092400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:20088800-20090200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr17:20088800-20090400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr17:20088800-20090400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr17:20088800-20090600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr17:20088800-20092200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr17:20088800-20092200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr17:20088800-20092200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr17:20088800-20092200	Weak transcription	K562	blood
33	chr17:20088800-20093000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr17:20089000-20090200	Weak transcription	A549	lung
35	chr17:20089000-20091000	Enhancers	Hela-S3	cervix
36	chr17:20089000-20092200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr17:20089000-20092400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr17:20089000-20092600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr17:20089000-20092800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr17:20089000-20097600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr17:20089200-20090400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:20089200-20092400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr17:20089200-20095000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr17:20089400-20091200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:20089600-20090200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr17:20089600-20091000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:20089600-20091200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:20089600-20091400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:20089600-20096400	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr17:20089600-20098000	Strong transcription	Monocytes-CD14+_RO01746	blood

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