Variant report

Variant	rs12451841
Chromosome Location	chr17:20004875-20004876
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	chr17:20002270..20005089-chr17:20012267..20015383,3	K562	blood:

Variant related genes	Relation type
ENSG00000225014	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10083830	0.87[AMR][1000 genomes]
rs10083840	0.90[AMR][1000 genomes]
rs11204422	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11654025	0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11867585	0.90[JPT][hapmap]
rs11869931	0.98[ASN][1000 genomes]
rs11870381	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11870673	0.83[ASN][1000 genomes]
rs12451216	0.93[ASN][1000 genomes]
rs12453332	0.95[ASN][1000 genomes]
rs12942179	0.80[CEU][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12947713	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12949710	0.98[ASN][1000 genomes]
rs1468953	0.98[ASN][1000 genomes]
rs1638526	0.90[JPT][hapmap]
rs17685923	0.98[ASN][1000 genomes]
rs17686798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[ASN][1000 genomes]
rs17759083	0.90[AMR][1000 genomes]
rs17759609	0.84[MEX][hapmap]
rs17759959	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1812934	0.83[MEX][hapmap]
rs2013441	0.88[MEX][hapmap]
rs2034110	1.00[JPT][hapmap]
rs2072337	0.90[JPT][hapmap]
rs2107566	0.83[MEX][hapmap]
rs2189710	0.83[MEX][hapmap]
rs2526475	0.83[MEX][hapmap]
rs2526480	0.83[MEX][hapmap]
rs2703774	0.83[MEX][hapmap]
rs2703804	0.83[MEX][hapmap]
rs2703815	0.83[MEX][hapmap]
rs2703817	0.83[MEX][hapmap]
rs28424266	0.90[JPT][hapmap]
rs34089239	0.83[MEX][hapmap]
rs34370440	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34756775	0.98[ASN][1000 genomes]
rs35041742	0.87[ASN][1000 genomes]
rs35124809	0.98[ASN][1000 genomes]
rs35156798	0.95[ASN][1000 genomes]
rs35191778	0.98[ASN][1000 genomes]
rs35244101	0.98[ASN][1000 genomes]
rs35493088	0.98[ASN][1000 genomes]
rs35770292	0.95[ASN][1000 genomes]
rs36051592	0.88[ASN][1000 genomes]
rs3850783	0.83[MEX][hapmap]
rs4141185	0.90[JPT][hapmap]
rs4341795	0.98[ASN][1000 genomes]
rs4346259	0.98[ASN][1000 genomes]
rs4350625	0.98[ASN][1000 genomes]
rs4471741	0.98[ASN][1000 genomes]
rs4570919	0.90[JPT][hapmap]
rs4588033	0.83[MEX][hapmap]
rs4924808	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs4924810	0.83[MEX][hapmap]
rs4925075	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs4925076	0.98[ASN][1000 genomes]
rs4925078	0.98[ASN][1000 genomes]
rs4925082	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925084	0.84[CEU][hapmap]
rs4925088	0.86[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57146223	0.82[ASN][1000 genomes]
rs62067488	0.98[ASN][1000 genomes]
rs6587207	1.00[JPT][hapmap]
rs7207459	1.00[JPT][hapmap]
rs7207611	0.83[MEX][hapmap]
rs7209653	0.90[JPT][hapmap]
rs7215803	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7224875	1.00[JPT][hapmap]
rs7225249	0.90[JPT][hapmap]
rs7503407	0.98[ASN][1000 genomes]
rs8066705	0.86[ASN][1000 genomes]
rs8068484	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs8074791	0.86[ASN][1000 genomes]
rs8075343	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8080190	1.00[JPT][hapmap]
rs8081817	0.98[ASN][1000 genomes]
rs888424	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs972966	0.90[ASN][1000 genomes]
rs9897328	0.83[MEX][hapmap]
rs9897653	0.90[JPT][hapmap]
rs9901125	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9901294	0.90[JPT][hapmap]
rs9904928	0.83[MEX][hapmap]
rs9915039	1.00[JPT][hapmap]
rs9944451	0.90[JPT][hapmap];0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12451841	AKAP10	cis	lymphoblastoid	seeQTL
rs12451841	CYTSB	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19993400-20006400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr17:19993800-20006400	Weak transcription	Esophagus	oesophagus
3	chr17:19993800-20008800	Weak transcription	GM12878-XiMat	blood
4	chr17:19999000-20006000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr17:19999000-20032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr17:19999200-20005000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr17:19999200-20008800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr17:19999400-20005000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr17:19999400-20005600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr17:19999400-20011800	Weak transcription	A549	lung
11	chr17:20000000-20005600	Weak transcription	Brain Substantia Nigra	brain
12	chr17:20000200-20006200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr17:20000600-20006600	Weak transcription	Ovary	ovary
14	chr17:20000800-20005000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr17:20002200-20005400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr17:20002200-20005800	Weak transcription	Brain Hippocampus Middle	brain
17	chr17:20002200-20018800	Weak transcription	Spleen	Spleen
18	chr17:20002200-20033400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr17:20002400-20005000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:20002400-20005400	Weak transcription	Brain Anterior Caudate	brain
21	chr17:20002400-20006400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:20002400-20013600	Weak transcription	Aorta	Aorta
23	chr17:20002600-20006400	Weak transcription	Brain Angular Gyrus	brain
24	chr17:20004000-20005000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr17:20004000-20013600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr17:20004600-20007000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr17:20004600-20008400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr17:20004800-20006200	Strong transcription	Adipose Nuclei	Adipose
29	chr17:20004800-20007600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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