Variant report

Variant	rs9908418
Chromosome Location	chr17:20214565-20214566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11868429	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs12051550	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12051865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
rs16942325	0.90[CEU][hapmap];0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16959946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16960717	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs16960730	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap]
rs16964352	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1971043	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs1971044	1.00[CHB][hapmap]
rs28550747	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3751979	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs3764436	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5025290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57110692	0.86[ASN][1000 genomes]
rs61660810	0.80[ASN][1000 genomes]
rs6587061	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
rs7213816	1.00[CHB][hapmap]
rs73981807	0.89[EUR][1000 genomes]
rs8077852	0.84[ASN][1000 genomes]
rs9889684	0.87[EUR][1000 genomes]
rs9895177	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9895295	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs9897161	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9897168	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9899514	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs9901102	0.86[ASN][1000 genomes]
rs9901357	0.89[EUR][1000 genomes]
rs9901484	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9902683	1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9908032	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9909156	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9911605	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs9913018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9913394	0.86[ASN][1000 genomes]
rs9914219	0.94[ASN][1000 genomes]
rs9941362	1.00[CHB][hapmap]
rs9941376	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers 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	53 gene(s)	inside rSNPs	diseases
8	nsv1065758	chr17:20141912-20464366	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv543262	chr17:20141912-20464366	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv1057389	chr17:20158343-20256498	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv427993	chr17:20171398-20482061	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	nsv520772	chr17:20184501-20522444	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	nsv521025	chr17:20198024-20514921	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9908418	AKAP10	cis	multi-tissue	Pritchard
rs9908418	CYTSB	cis	parietal	SCAN
rs9908418	ALDH3A1	cis	parietal	SCAN
rs9908418	AKAP10	cis	Whole Blood	GTEx
rs9908418	USP32P3	cis	Nerve Tibial	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20187800-20223800	Weak transcription	Pancreas	Pancrea
2	chr17:20201000-20220000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:20204400-20216800	Weak transcription	Gastric	stomach
4	chr17:20210800-20223800	Weak transcription	Colonic Mucosa	Colon
5	chr17:20210800-20223800	Weak transcription	Esophagus	oesophagus
6	chr17:20211000-20215800	Weak transcription	Brain Angular Gyrus	brain
7	chr17:20211000-20215800	Weak transcription	Brain Substantia Nigra	brain
8	chr17:20211000-20216000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:20211000-20216600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:20211000-20216600	Weak transcription	Aorta	Aorta
11	chr17:20211000-20216800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:20211000-20216800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr17:20211000-20217000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr17:20211000-20217000	Weak transcription	NHEK	skin
15	chr17:20211000-20217200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:20211000-20217200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr17:20211000-20218600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:20211000-20218600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr17:20211000-20219600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr17:20211000-20223000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr17:20211000-20223800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr17:20211000-20223800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:20211000-20224000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr17:20211000-20224000	Weak transcription	HMEC	breast
25	chr17:20211200-20215800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr17:20211200-20216000	Weak transcription	GM12878-XiMat	blood
27	chr17:20211200-20216000	Weak transcription	NH-A	brain
28	chr17:20211200-20217000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr17:20211200-20217200	Weak transcription	Fetal Brain Female	brain
30	chr17:20211200-20221600	Weak transcription	Small Intestine	intestine
31	chr17:20211200-20223800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr17:20211200-20224000	Weak transcription	Fetal Intestine Large	intestine
33	chr17:20211400-20220800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr17:20211400-20224000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:20211600-20217400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:20211600-20218000	Weak transcription	Fetal Intestine Small	intestine
37	chr17:20211600-20221800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:20211600-20224000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr17:20212200-20216600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr17:20212200-20222000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr17:20212400-20219800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr17:20212600-20216600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr17:20212600-20217000	Weak transcription	Osteobl	bone
44	chr17:20212800-20215800	Weak transcription	Brain Anterior Caudate	brain
45	chr17:20212800-20218400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr17:20213000-20214600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr17:20213000-20216000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr17:20213000-20217200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:20213000-20217200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr17:20213000-20217400	Weak transcription	Brain Germinal Matrix	brain

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