Variant report

Variant	rs9895177
Chromosome Location	chr17:20207594-20207595
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12051550	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12051865	0.86[ASN][1000 genomes]
rs16942325	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16959946	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16964352	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28550747	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3764436	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5025290	0.93[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	0.86[ASN][1000 genomes]
rs73981803	0.89[EUR][1000 genomes]
rs73981807	0.89[EUR][1000 genomes]
rs8077852	0.84[ASN][1000 genomes]
rs9889684	0.87[EUR][1000 genomes]
rs9897161	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9897168	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9899514	0.80[ASN][1000 genomes]
rs9901102	0.86[ASN][1000 genomes]
rs9901357	0.89[EUR][1000 genomes]
rs9901484	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9902683	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9908032	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9908418	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9909156	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9911879	0.89[EUR][1000 genomes]
rs9913018	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9913394	0.86[ASN][1000 genomes]
rs9914219	0.94[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9895177	AKAP10	cis	Whole Blood	GTEx
rs9895177	USP32P3	cis	Nerve Tibial	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20136400-20209800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:20170400-20209600	Weak transcription	HMEC	breast
3	chr17:20185200-20209800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:20186000-20209400	Weak transcription	Spleen	Spleen
5	chr17:20186200-20209800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:20187800-20223800	Weak transcription	Pancreas	Pancrea
7	chr17:20188200-20208400	Weak transcription	NHEK	skin
8	chr17:20188600-20209800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:20188600-20209800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr17:20190000-20208600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr17:20197800-20209800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr17:20200000-20209600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr17:20200200-20207600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr17:20200800-20209200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr17:20200800-20209400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr17:20201000-20208000	Weak transcription	A549	lung
17	chr17:20201000-20220000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr17:20201200-20208600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr17:20201200-20209400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr17:20201400-20208000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:20201400-20208800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr17:20201400-20209800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr17:20201800-20209400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr17:20202000-20208000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr17:20202400-20209200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:20203800-20208200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr17:20203800-20208400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr17:20203800-20209600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr17:20204000-20207800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:20204000-20208200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:20204000-20208400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr17:20204000-20209800	Weak transcription	Fetal Intestine Small	intestine
33	chr17:20204200-20207800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr17:20204200-20208600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:20204200-20209800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:20204200-20209800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr17:20204400-20209800	Weak transcription	Aorta	Aorta
38	chr17:20204400-20209800	Weak transcription	Fetal Intestine Large	intestine
39	chr17:20204400-20216800	Weak transcription	Gastric	stomach
40	chr17:20204600-20207600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr17:20204600-20208400	Weak transcription	Adipose Nuclei	Adipose
42	chr17:20204600-20209800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr17:20204800-20209800	Weak transcription	HSMM	muscle
44	chr17:20204800-20209800	Weak transcription	HSMMtube	muscle
45	chr17:20204800-20212200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr17:20205000-20207800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:20205000-20207800	Weak transcription	NH-A	brain
48	chr17:20205400-20208000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr17:20205800-20207600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr17:20205800-20208200	Weak transcription	Ovary	ovary

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