Variant report

Variant	rs17759959
Chromosome Location	chr17:20024095-20024096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 183 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:173)

rs_ID	r²[population]
rs1009082	0.85[CEU][hapmap]
rs10438824	0.85[CEU][hapmap]
rs11204422	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11654025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11867585	0.83[JPT][hapmap]
rs11869931	0.90[ASN][1000 genomes]
rs11870147	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11870381	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11870673	0.82[ASN][1000 genomes]
rs11871827	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11871945	0.84[EUR][1000 genomes]
rs12451216	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12451841	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12453332	0.87[ASN][1000 genomes]
rs12937827	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12941200	0.80[AMR][1000 genomes]
rs12942179	0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs12947713	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12947950	0.85[CEU][hapmap]
rs12948178	0.80[AMR][1000 genomes]
rs12949485	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs12949710	0.90[ASN][1000 genomes]
rs12952398	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1373147	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1468953	0.90[ASN][1000 genomes]
rs1544421	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1561974	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1638526	0.90[JPT][hapmap]
rs17685923	0.90[ASN][1000 genomes]
rs17686622	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs17686798	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17686839	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17759923	0.87[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1812934	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1985810	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1992562	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2005722	0.87[EUR][1000 genomes]
rs2013441	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2013576	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2034109	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2034110	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2058971	1.00[CEU][hapmap]
rs2072337	0.90[JPT][hapmap]
rs2080673	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2107566	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2120282	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2158473	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2165897	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2189710	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2243732	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2263175	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2386429	0.84[EUR][1000 genomes]
rs2386485	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526458	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526460	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526462	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526464	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2526467	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2526468	0.85[CEU][hapmap]
rs2526469	0.85[CEU][hapmap]
rs2526471	0.85[CEU][hapmap]
rs2526472	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526474	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526475	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2526480	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2526483	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2526484	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2526488	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526490	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2526491	0.81[CEU][hapmap]
rs2703772	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703773	0.85[CEU][hapmap]
rs2703774	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703778	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703780	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703782	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703785	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703787	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2703789	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703790	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2703791	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2703792	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2703794	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2703799	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2703801	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2703802	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2703804	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2703806	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2703808	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703810	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2703813	0.85[CEU][hapmap]
rs2703815	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703816	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703817	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703818	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2703820	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2703821	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28424266	0.90[JPT][hapmap]
rs34089239	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34370440	0.92[ASN][1000 genomes]
rs34644796	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34712254	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34756775	0.90[ASN][1000 genomes]
rs35041742	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35124809	0.90[ASN][1000 genomes]
rs35156798	0.87[ASN][1000 genomes]
rs35191778	0.90[ASN][1000 genomes]
rs35244101	0.90[ASN][1000 genomes]
rs35493088	0.90[ASN][1000 genomes]
rs35770292	0.87[ASN][1000 genomes]
rs36051592	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3850783	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3850784	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3850785	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3940274	0.82[ASN][1000 genomes]
rs4341795	0.90[ASN][1000 genomes]
rs4346259	0.90[ASN][1000 genomes]
rs4350625	0.90[ASN][1000 genomes]
rs4471741	0.90[ASN][1000 genomes]
rs4570919	0.82[JPT][hapmap]
rs4588033	0.96[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924808	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4924809	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4924810	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4925075	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4925076	0.90[ASN][1000 genomes]
rs4925078	0.90[ASN][1000 genomes]
rs4925082	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4925088	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4925089	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57146223	0.87[ASN][1000 genomes]
rs62067488	0.90[ASN][1000 genomes]
rs62067558	0.80[AMR][1000 genomes]
rs6587063	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6587064	0.82[CEU][hapmap]
rs6587207	1.00[JPT][hapmap]
rs7207459	1.00[JPT][hapmap]
rs7207611	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7207817	0.85[CEU][hapmap]
rs7209653	0.90[JPT][hapmap]
rs7215803	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7223363	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7224875	1.00[JPT][hapmap]
rs7225249	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7503407	0.90[ASN][1000 genomes]
rs8066705	0.85[ASN][1000 genomes]
rs8068484	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8068720	1.00[CEU][hapmap]
rs8070401	0.88[CEU][hapmap]
rs8071665	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs8074047	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8074791	0.85[ASN][1000 genomes]
rs8075343	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8079701	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs8080190	1.00[JPT][hapmap]
rs8081817	0.90[ASN][1000 genomes]
rs888424	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9325894	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs972966	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9892630	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9896221	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9896709	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9897328	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9897653	0.83[JPT][hapmap]
rs9900166	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9901125	0.92[ASN][1000 genomes]
rs9901294	0.90[JPT][hapmap]
rs9904928	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9905493	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9915039	1.00[JPT][hapmap]
rs9915059	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9915628	0.82[EUR][1000 genomes]
rs9944451	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17759959	AKAP10	cis	Lymphoblastoid	GTEx
rs17759959	SPECC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 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	chr17:20007400-20024200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:20009200-20024200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr17:20014400-20024200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:20014400-20024400	Weak transcription	Ovary	ovary
7	chr17:20014400-20024800	Weak transcription	Aorta	Aorta
8	chr17:20014400-20025200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:20014600-20028800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr17:20016000-20028800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:20016400-20024400	Weak transcription	Adipose Nuclei	Adipose
12	chr17:20016400-20028600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:20017400-20026200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr17:20018200-20025200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:20018400-20025000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr17:20020600-20024200	Weak transcription	Brain Angular Gyrus	brain
17	chr17:20020600-20024200	Weak transcription	Brain Anterior Caudate	brain
18	chr17:20020600-20024200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr17:20020600-20024200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr17:20020600-20024800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr17:20020600-20025200	Weak transcription	A549	lung
22	chr17:20023200-20025000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr17:20023600-20026000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr17:20023600-20026600	Enhancers	Fetal Brain Male	brain
25	chr17:20023800-20025800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:20023800-20026000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr17:20024000-20024200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr17:20024000-20025200	Enhancers	Brain Hippocampus Middle	brain
29	chr17:20024000-20025200	Enhancers	Brain Substantia Nigra	brain
30	chr17:20024000-20025600	Enhancers	Brain Germinal Matrix	brain
31	chr17:20024000-20026000	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links