Variant report

Variant	rs28550747
Chromosome Location	chr17:20178312-20178313
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11868429	0.90[ASN][1000 genomes]
rs12051550	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12051865	0.90[ASN][1000 genomes]
rs13339684	0.88[EUR][1000 genomes]
rs16942325	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16959946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16960660	0.89[EUR][1000 genomes]
rs16960678	0.89[EUR][1000 genomes]
rs16960717	0.88[AMR][1000 genomes]
rs16964352	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1971044	0.86[AMR][1000 genomes]
rs28644386	0.88[EUR][1000 genomes]
rs3751979	0.90[ASN][1000 genomes]
rs3764436	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5025290	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56138907	0.89[EUR][1000 genomes]
rs57110692	0.90[ASN][1000 genomes]
rs61660810	0.92[ASN][1000 genomes]
rs6587061	0.90[ASN][1000 genomes]
rs7207458	0.90[ASN][1000 genomes]
rs7210439	0.89[EUR][1000 genomes]
rs7225605	0.89[EUR][1000 genomes]
rs73981803	0.89[EUR][1000 genomes]
rs73981807	0.89[EUR][1000 genomes]
rs73981849	0.82[AMR][1000 genomes]
rs73984564	0.88[EUR][1000 genomes]
rs73984568	0.88[EUR][1000 genomes]
rs73984571	0.89[EUR][1000 genomes]
rs73984573	0.89[EUR][1000 genomes]
rs8077852	0.88[ASN][1000 genomes]
rs9889684	0.87[EUR][1000 genomes]
rs9895177	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9897161	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9897168	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9899514	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9901102	0.90[ASN][1000 genomes]
rs9901357	0.89[EUR][1000 genomes]
rs9901484	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9902683	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9908032	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9908418	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9909156	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9911879	0.89[EUR][1000 genomes]
rs9913018	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9914219	0.82[ASN][1000 genomes]
rs9916729	0.89[EUR][1000 genomes]

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	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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28550747	USP32P3	cis	Nerve Tibial	GTEx
rs28550747	AKAP10	cis	Whole Blood	GTEx

Chromatin state (count:87 , 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	chr17:20151600-20190000	Weak transcription	Colonic Mucosa	Colon
3	chr17:20161800-20180200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:20162000-20187600	Weak transcription	Pancreas	Pancrea
5	chr17:20164000-20200200	Weak transcription	Fetal Intestine Large	intestine
6	chr17:20164000-20205600	Weak transcription	Esophagus	oesophagus
7	chr17:20164200-20200200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr17:20164400-20202200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr17:20164600-20203800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr17:20164600-20204000	Weak transcription	Gastric	stomach
11	chr17:20165000-20182000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr17:20165800-20180400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr17:20166000-20185000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr17:20166600-20187400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr17:20167200-20183200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:20167400-20187600	Weak transcription	A549	lung
17	chr17:20167400-20200200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr17:20168200-20182000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr17:20168200-20182400	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr17:20170000-20182000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr17:20170400-20209600	Weak transcription	HMEC	breast
22	chr17:20170600-20179600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr17:20171200-20179000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr17:20171200-20200200	Weak transcription	Lung	lung
25	chr17:20171400-20187400	Weak transcription	HSMM	muscle
26	chr17:20171400-20187800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr17:20171600-20181600	Weak transcription	HSMMtube	muscle
28	chr17:20171600-20183800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr17:20173200-20178600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr17:20173400-20180200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:20173400-20180200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr17:20173400-20180200	Weak transcription	Spleen	Spleen
33	chr17:20173400-20187600	Weak transcription	Aorta	Aorta
34	chr17:20173400-20197600	Weak transcription	Brain Germinal Matrix	brain
35	chr17:20173600-20179800	Weak transcription	Adipose Nuclei	Adipose
36	chr17:20173600-20180000	Weak transcription	Brain Substantia Nigra	brain
37	chr17:20173600-20180200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr17:20173800-20180200	Weak transcription	Ovary	ovary
39	chr17:20174000-20180600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr17:20174400-20200200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr17:20174600-20179800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr17:20174800-20179000	Weak transcription	GM12878-XiMat	blood
43	chr17:20174800-20188400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr17:20175000-20181600	Weak transcription	Osteobl	bone
45	chr17:20175000-20187800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr17:20175000-20200200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr17:20175400-20178800	Weak transcription	Brain Hippocampus Middle	brain
48	chr17:20176400-20183000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:20176400-20183000	Weak transcription	Fetal Intestine Small	intestine
50	chr17:20176600-20178800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links