Variant report

Variant	rs5025290
Chromosome Location	chr17:20205817-20205818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11868429	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
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];1.00[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];0.94[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];0.94[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];0.90[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];0.96[ASN][1000 genomes]
rs3751979	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.86[ASN][1000 genomes]
rs3764436	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56138907	0.89[EUR][1000 genomes]
rs57110692	0.94[ASN][1000 genomes]
rs61660810	0.88[ASN][1000 genomes]
rs6587061	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[ASN][1000 genomes]
rs7207458	0.86[ASN][1000 genomes]
rs7210439	0.89[EUR][1000 genomes]
rs7213816	1.00[CHB][hapmap]
rs7215097	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap]
rs7225605	0.89[EUR][1000 genomes]
rs73981803	0.89[EUR][1000 genomes]
rs73981807	0.89[EUR][1000 genomes]
rs8077852	0.92[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];0.92[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];0.94[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];0.88[ASN][1000 genomes]
rs9901102	0.94[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]
rs9908418	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]
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]
rs9911879	0.89[EUR][1000 genomes]
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]
rs9914219	0.86[ASN][1000 genomes]
rs9941362	1.00[CHB][hapmap]
rs9941376	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
4	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
5	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
6	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
7	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
8	nsv1063833	chr17:20088333-20206601	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	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
10	nsv1062124	chr17:20139384-20206601	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv543261	chr17:20139384-20206601	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	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
17	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
18	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5025290	ALDH3A1	cis	parietal	SCAN
rs5025290	USP32P3	cis	Nerve Tibial	GTEx
rs5025290	CYTSB	cis	parietal	SCAN
rs5025290	AKAP10	cis	Whole Blood	GTEx

Chromatin state (count:79 , 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	chr17:20185600-20206800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr17:20186000-20209400	Weak transcription	Spleen	Spleen
6	chr17:20186200-20209800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:20187800-20223800	Weak transcription	Pancreas	Pancrea
8	chr17:20188200-20208400	Weak transcription	NHEK	skin
9	chr17:20188600-20209800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:20188600-20209800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr17:20190000-20208600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr17:20197800-20209800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr17:20200000-20209600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr17:20200200-20206800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr17:20200200-20207000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr17:20200200-20207400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr17:20200200-20207600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:20200400-20207400	Strong transcription	Hela-S3	cervix
19	chr17:20200800-20209200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr17:20200800-20209400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr17:20201000-20208000	Weak transcription	A549	lung
22	chr17:20201000-20220000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr17:20201200-20208600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr17:20201200-20209400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr17:20201400-20208000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:20201400-20208800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr17:20201400-20209800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr17:20201800-20209400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr17:20202000-20208000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr17:20202400-20206800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr17:20202400-20209200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:20203000-20206200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr17:20203000-20206800	Enhancers	Fetal Stomach	stomach
34	chr17:20203200-20206600	Enhancers	Brain Hippocampus Middle	brain
35	chr17:20203200-20206800	Enhancers	Brain Cingulate Gyrus	brain
36	chr17:20203400-20206200	Enhancers	Brain Angular Gyrus	brain
37	chr17:20203400-20206800	Enhancers	Colon Smooth Muscle	Colon
38	chr17:20203800-20206200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr17:20203800-20208200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr17:20203800-20208400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr17:20203800-20209600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:20204000-20207800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:20204000-20208200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr17:20204000-20208400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr17:20204000-20209800	Weak transcription	Fetal Intestine Small	intestine
46	chr17:20204200-20207200	Weak transcription	Placenta	Placenta
47	chr17:20204200-20207800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr17:20204200-20208600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr17:20204200-20209800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr17:20204200-20209800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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