Variant report

Variant	rs9889684
Chromosome Location	chr17:20003971-20003972
allele	A/T
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: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12051550	0.88[EUR][1000 genomes]
rs13339684	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16942325	0.87[EUR][1000 genomes]
rs16959946	0.87[EUR][1000 genomes]
rs16960660	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16960678	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16964352	0.82[EUR][1000 genomes]
rs28550747	0.87[EUR][1000 genomes]
rs28567541	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28622601	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28644386	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3764436	0.94[EUR][1000 genomes]
rs5025290	0.87[EUR][1000 genomes]
rs56138907	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7210439	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7219770	0.91[ASN][1000 genomes]
rs7223910	0.91[ASN][1000 genomes]
rs7225605	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73981803	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73981807	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73984564	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73984568	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73984571	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73984573	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9895177	0.87[EUR][1000 genomes]
rs9897161	0.89[EUR][1000 genomes]
rs9897168	0.89[EUR][1000 genomes]
rs9901357	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9901484	0.89[EUR][1000 genomes]
rs9902683	0.94[EUR][1000 genomes]
rs9908032	0.92[EUR][1000 genomes]
rs9908418	0.87[EUR][1000 genomes]
rs9909156	0.87[EUR][1000 genomes]
rs9911879	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913018	0.89[EUR][1000 genomes]
rs9916729	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]

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
rs9889684	USP32P3	cis	Nerve Tibial	GTEx
rs9889684	AKAP10	cis	Whole Blood	GTEx

Chromatin state (count:31 , 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	chr17:19999400-20004400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:19999400-20005000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr17:19999400-20005600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr17:19999400-20011800	Weak transcription	A549	lung
12	chr17:20000000-20005600	Weak transcription	Brain Substantia Nigra	brain
13	chr17:20000200-20006200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr17:20000600-20006600	Weak transcription	Ovary	ovary
15	chr17:20000800-20005000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr17:20002000-20004200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr17:20002200-20005400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr17:20002200-20005800	Weak transcription	Brain Hippocampus Middle	brain
19	chr17:20002200-20018800	Weak transcription	Spleen	Spleen
20	chr17:20002200-20033400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:20002400-20004800	Weak transcription	Adipose Nuclei	Adipose
22	chr17:20002400-20005000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:20002400-20005400	Weak transcription	Brain Anterior Caudate	brain
24	chr17:20002400-20006400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:20002400-20013600	Weak transcription	Aorta	Aorta
26	chr17:20002600-20006400	Weak transcription	Brain Angular Gyrus	brain
27	chr17:20003400-20004000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr17:20003400-20004000	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr17:20003400-20004000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr17:20003800-20004600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr17:20003800-20004800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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