Variant report

Variant	rs13339684
Chromosome Location	chr17:19977211-19977212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12051550	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs16942325	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs16959946	1.00[CEU][hapmap];0.80[CHB][hapmap];0.88[EUR][1000 genomes]
rs16960660	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16960678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16964352	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs28550747	0.88[EUR][1000 genomes]
rs28567541	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28622601	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28644386	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3764436	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs56138907	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7210439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7219770	0.91[ASN][1000 genomes]
rs7221750	0.80[YRI][hapmap]
rs7223910	0.91[ASN][1000 genomes]
rs7225605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73981803	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73981807	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73984564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73984568	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73984571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73984573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9889684	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9897161	0.88[EUR][1000 genomes]
rs9897168	0.88[EUR][1000 genomes]
rs9901357	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9901484	0.88[EUR][1000 genomes]
rs9902683	0.88[EUR][1000 genomes]
rs9908032	0.86[EUR][1000 genomes]
rs9909156	0.86[EUR][1000 genomes]
rs9911879	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9913018	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9916729	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[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	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	nsv1066594	chr17:19947874-19986671	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv543259	chr17:19947874-19986671	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	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
15	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13339684	AKAP10	cis	Whole Blood	GTEx
rs13339684	USP32P3	cis	Nerve Tibial	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19974200-19978000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr17:19975200-19977600	Enhancers	K562	blood
3	chr17:19975400-19978000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:19975400-19978800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr17:19975600-19977600	Enhancers	Brain Germinal Matrix	brain
6	chr17:19975800-19977600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr17:19975800-19978000	Enhancers	NHDF-Ad	bronchial
8	chr17:19975800-19978200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:19976000-19978200	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr17:19976000-19978200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:19976200-19977800	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr17:19976200-19978000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:19976200-19978200	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr17:19976200-19988000	Weak transcription	Gastric	stomach
15	chr17:19976200-19989400	Weak transcription	Lung	lung
16	chr17:19976400-19977600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr17:19976400-19977600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr17:19976400-19977800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr17:19976400-19978000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr17:19976400-19978000	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr17:19976400-19978200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr17:19976400-19978200	Flanking Active TSS	GM12878-XiMat	blood
23	chr17:19976600-19977600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:19976600-19977600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:19976600-19978000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr17:19976600-19978000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:19976600-19978200	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr17:19976600-19978200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr17:19976600-19978200	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr17:19976600-19978200	Active TSS	Monocytes-CD14+_RO01746	blood
31	chr17:19976800-19977400	Flanking Active TSS	Fetal Thymus	thymus
32	chr17:19976800-19977600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr17:19976800-19977600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr17:19976800-19977600	Enhancers	Esophagus	oesophagus
35	chr17:19976800-19977600	Flanking Active TSS	Osteobl	bone
36	chr17:19976800-19977800	Active TSS	Primary monocytes fromperipheralblood	blood
37	chr17:19976800-19978000	Active TSS	Brain Angular Gyrus	brain
38	chr17:19976800-19978000	Active TSS	Brain Anterior Caudate	brain
39	chr17:19976800-19978000	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr17:19976800-19978000	Enhancers	Fetal Lung	lung
41	chr17:19976800-19978000	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr17:19976800-19978800	Active TSS	Brain Hippocampus Middle	brain
43	chr17:19976800-19979000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr17:19977000-19977400	Enhancers	Primary B cells from peripheral blood	blood
45	chr17:19977000-19977400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr17:19977000-19977400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr17:19977000-19977400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr17:19977000-19977400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr17:19977000-19977400	Bivalent/Poised TSS	Liver	Liver
50	chr17:19977000-19977400	Active TSS	Fetal Muscle Leg	muscle

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