Variant report

Variant	rs9896190
Chromosome Location	chr17:20102925-20102926
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	chr17:20080334..20082016-chr17:20102428..20104693,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11868429	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12051550	0.86[ASN][1000 genomes]
rs12051844	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12051865	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16960700	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16960715	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16960717	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16960730	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16960735	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1971043	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1971044	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3751979	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57110692	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61141789	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61660810	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587060	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6587061	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587218	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587221	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7207458	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7211948	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7213349	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7213816	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7215097	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7215432	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7218859	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73299658	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73301548	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73309111	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73981849	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8076627	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8077051	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8077852	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9899514	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9901102	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9901484	0.82[ASN][1000 genomes]
rs9905976	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9908032	0.86[ASN][1000 genomes]
rs9909156	0.86[ASN][1000 genomes]
rs9911605	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9913018	0.82[ASN][1000 genomes]
rs9913394	0.90[EUR][1000 genomes]
rs9914219	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9941362	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9941376	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
11	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
12	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
13	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
14	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
15	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
rs9896190	AKAP10	cis	Whole Blood	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20094200-20103800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr17:20094200-20105400	Weak transcription	Gastric	stomach
3	chr17:20094600-20105400	Weak transcription	K562	blood
4	chr17:20094800-20105600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:20095400-20104800	Weak transcription	HMEC	breast
6	chr17:20096000-20103600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr17:20096800-20103400	Weak transcription	Brain Angular Gyrus	brain
8	chr17:20097600-20107800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr17:20099800-20103800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:20099800-20107200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr17:20100000-20103800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:20100000-20104000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:20101000-20103800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr17:20101600-20103600	Weak transcription	Brain Anterior Caudate	brain
15	chr17:20101600-20103800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr17:20101600-20103800	Weak transcription	Ovary	ovary
17	chr17:20101600-20107600	Enhancers	Hela-S3	cervix
18	chr17:20101600-20108200	Weak transcription	Aorta	Aorta
19	chr17:20101800-20103600	Weak transcription	Brain Substantia Nigra	brain
20	chr17:20101800-20103800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr17:20101800-20107000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr17:20102000-20103400	Weak transcription	Brain Hippocampus Middle	brain
23	chr17:20102000-20118400	Weak transcription	Pancreas	Pancrea
24	chr17:20102200-20104400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr17:20102200-20105000	Weak transcription	GM12878-XiMat	blood
26	chr17:20102400-20103000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr17:20102400-20103400	Weak transcription	A549	lung
28	chr17:20102400-20106400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:20102400-20107000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr17:20102400-20107200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr17:20102400-20108200	Weak transcription	Adipose Nuclei	Adipose
32	chr17:20102400-20115200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr17:20102600-20108200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:20102800-20103000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr17:20102800-20103400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:20102800-20103800	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links