Variant report

Variant	rs17759609
Chromosome Location	chr17:19992514-19992515
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19991773..19994998-chr2:209032034..209035004,3	K562	blood:
2	chr17:19991747..19994521-chr2:209032147..209035018,4	K562	blood:

Extended variants
information (count: 137 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10083830	1.00[ASN][1000 genomes]
rs10083840	1.00[ASN][1000 genomes]
rs1009082	1.00[CHB][hapmap]
rs10438824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs11658169	1.00[LWK][hapmap]
rs11869931	0.91[AMR][1000 genomes]
rs12449914	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450857	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs12451841	0.84[MEX][hapmap]
rs12453332	0.90[AMR][1000 genomes]
rs12453720	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs12935996	1.00[LWK][hapmap]
rs12937327	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12941200	0.83[AMR][1000 genomes]
rs12943904	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12946508	0.80[EUR][1000 genomes]
rs12947713	0.91[AMR][1000 genomes]
rs12947950	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs12948178	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12949485	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12949710	0.91[AMR][1000 genomes]
rs1468953	0.91[AMR][1000 genomes]
rs1544421	1.00[CHB][hapmap]
rs1638527	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1638528	0.81[CEU][hapmap]
rs16960550	1.00[LWK][hapmap]
rs17604987	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs17685923	0.91[AMR][1000 genomes]
rs17686622	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17686839	1.00[CHB][hapmap]
rs17759041	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17759083	1.00[ASN][1000 genomes]
rs1812934	1.00[CHB][hapmap]
rs2013576	1.00[CHB][hapmap]
rs203467	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs203475	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs203478	0.83[CEU][hapmap]
rs203480	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs2107566	1.00[CHB][hapmap]
rs2108981	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs2158473	1.00[CHB][hapmap]
rs2189710	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2263175	1.00[CHB][hapmap]
rs2386485	1.00[CHB][hapmap]
rs2526460	1.00[CHB][hapmap]
rs2526462	1.00[CHB][hapmap]
rs2526467	1.00[CHB][hapmap]
rs2526468	1.00[CHB][hapmap]
rs2526469	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap]
rs2526471	1.00[CHB][hapmap]
rs2526474	1.00[CHB][hapmap]
rs2526475	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2526480	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2526484	1.00[CHB][hapmap]
rs2526491	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap]
rs2703772	1.00[CHB][hapmap]
rs2703773	1.00[CHB][hapmap]
rs2703774	1.00[CHB][hapmap]
rs2703782	1.00[CHB][hapmap]
rs2703790	1.00[CHB][hapmap]
rs2703791	1.00[CHB][hapmap]
rs2703792	1.00[CHB][hapmap]
rs2703794	1.00[CHB][hapmap]
rs2703799	1.00[CHB][hapmap]
rs2703801	1.00[CHB][hapmap]
rs2703802	1.00[CHB][hapmap]
rs2703804	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2703806	1.00[CHB][hapmap]
rs2703808	1.00[CHB][hapmap]
rs2703813	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap]
rs2703815	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2703816	1.00[CHB][hapmap]
rs2703817	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2703818	1.00[CHB][hapmap]
rs2703821	1.00[CHB][hapmap]
rs34089239	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs34756775	0.91[AMR][1000 genomes]
rs35124809	0.91[AMR][1000 genomes]
rs35156798	0.91[AMR][1000 genomes]
rs35191778	0.91[AMR][1000 genomes]
rs35244101	0.91[AMR][1000 genomes]
rs35317166	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35493088	0.91[AMR][1000 genomes]
rs35770292	0.91[AMR][1000 genomes]
rs35915823	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850783	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs3850784	1.00[CHB][hapmap]
rs3850785	1.00[CHB][hapmap]
rs3862151	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341795	0.91[AMR][1000 genomes]
rs4346259	0.91[AMR][1000 genomes]
rs4350625	0.91[AMR][1000 genomes]
rs4471741	0.90[AMR][1000 genomes]
rs4588033	1.00[CHB][hapmap]
rs4924802	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924809	1.00[CHB][hapmap]
rs4924810	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4925054	1.00[CHB][hapmap]
rs4925071	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925074	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925075	0.91[GIH][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes]
rs4925076	0.91[AMR][1000 genomes]
rs4925078	0.91[AMR][1000 genomes]
rs4925082	0.84[MEX][hapmap]
rs4925084	1.00[CHB][hapmap];0.94[AMR][1000 genomes]
rs56371654	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62067488	0.91[AMR][1000 genomes]
rs62067558	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7209653	0.87[CEU][hapmap];0.87[MEX][hapmap]
rs7215803	0.87[MEX][hapmap]
rs7503407	0.91[AMR][1000 genomes]
rs8068484	0.90[AMR][1000 genomes]
rs8075343	0.91[AMR][1000 genomes]
rs8079923	0.83[CEU][hapmap]
rs8080827	1.00[CHB][hapmap]
rs8081817	0.91[AMR][1000 genomes]
rs850622	0.83[CEU][hapmap];1.00[CHD][hapmap]
rs888424	0.84[MEX][hapmap]
rs9896221	1.00[CHB][hapmap]
rs9896709	1.00[CHB][hapmap]
rs9897328	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9901294	0.87[CEU][hapmap];0.87[MEX][hapmap]
rs9904928	1.00[CHB][hapmap]
rs9905493	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv907872	chr17:19945841-19996140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1056224	chr17:19946604-19993026	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv543258	chr17:19946604-19993026	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	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
13	esv2762522	chr17:19976462-19996429	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17759609	AKAP10	cis	lymphoblastoid	seeQTL
rs17759609	AKAP10	cis	multi-tissue	Pritchard
rs17759609	CYTSB	cis	cerebellum	SCAN
rs17759609	MYO15A	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:19980600-19994600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr17:19981200-19993000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:19982600-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:19983200-19993400	Weak transcription	Spleen	Spleen
6	chr17:19985600-19993000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:19986200-19993000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:19987000-19994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr17:19988600-19993200	Weak transcription	GM12878-XiMat	blood
10	chr17:19988600-19994600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:19988800-19994600	Weak transcription	Right Atrium	heart
12	chr17:19989000-19994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr17:19989200-19994200	Weak transcription	Osteobl	bone
14	chr17:19989400-19994200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr17:19989600-19994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr17:19990000-19993000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr17:19990000-19995600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:19990200-19993000	Weak transcription	Left Ventricle	heart
19	chr17:19990200-19993400	Weak transcription	Esophagus	oesophagus
20	chr17:19990200-19993600	Weak transcription	NHDF-Ad	bronchial
21	chr17:19990200-19994000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr17:19990200-19994000	Weak transcription	Ovary	ovary
23	chr17:19990200-19994000	Weak transcription	Right Ventricle	heart
24	chr17:19990200-19994000	Weak transcription	NH-A	brain
25	chr17:19990200-19994600	Weak transcription	Brain Anterior Caudate	brain
26	chr17:19990200-19994600	Weak transcription	Brain Hippocampus Middle	brain
27	chr17:19990200-19994600	Weak transcription	Brain Substantia Nigra	brain
28	chr17:19990200-19994800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr17:19990200-19995000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:19990200-19998800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr17:19990400-19994600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr17:19990400-19994600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr17:19990600-19994000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:19990600-19995000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr17:19991200-19993200	Weak transcription	Adipose Nuclei	Adipose
36	chr17:19991200-19993400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:19991200-19994800	Weak transcription	Brain Angular Gyrus	brain
38	chr17:19991200-19995000	Weak transcription	A549	lung
39	chr17:19991200-19996800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr17:19991400-19994000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:19991600-19992800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr17:19991600-19993200	Weak transcription	Fetal Muscle Leg	muscle
43	chr17:19991800-19992600	Enhancers	Aorta	Aorta
44	chr17:19992400-19992600	Genic enhancers	Monocytes-CD14+_RO01746	blood
45	chr17:19992400-19993400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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