Variant report

Variant	rs17841999
Chromosome Location	chr20:41241888-41241889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:41235856..41237826-chr20:41240786..41243321,2	K562	blood:

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1040480	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11086845	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11086846	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1157668	0.88[CEU][hapmap]
rs11696144	0.88[CEU][hapmap]
rs11697778	0.80[CEU][hapmap]
rs11699493	0.82[EUR][1000 genomes]
rs11699599	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs12106100	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs13038923	0.88[CHB][hapmap]
rs17810209	0.83[CEU][hapmap]
rs17810239	0.81[CHD][hapmap]
rs1883843	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2223541	0.88[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap]
rs2867487	0.87[CEU][hapmap]
rs2867488	0.80[ASW][hapmap];0.88[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap]
rs4508660	0.88[CEU][hapmap]
rs55780401	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57742605	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60154566	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6016852	0.81[CHD][hapmap]
rs6016854	0.83[CHD][hapmap]
rs6016855	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6030350	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6030353	0.82[CEU][hapmap]
rs6030354	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs6030360	0.82[CEU][hapmap]
rs6030363	0.88[GIH][hapmap]
rs6030366	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs6030367	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6030368	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6030370	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs6030372	0.83[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap]
rs6030380	0.81[CHD][hapmap]
rs6030382	0.83[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap]
rs6030384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6030385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6030386	0.92[EUR][1000 genomes]
rs6030388	0.88[CEU][hapmap]
rs6030390	0.88[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs6093685	0.88[CHB][hapmap]
rs6093686	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs6093690	0.88[CHB][hapmap]
rs6093699	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6093701	0.87[AMR][1000 genomes]
rs6093705	0.84[CHD][hapmap]
rs6102923	0.82[CEU][hapmap]
rs6102924	0.82[CEU][hapmap]
rs6102925	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs6102926	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs6102929	0.88[CHB][hapmap]
rs6102932	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs6102933	0.88[CHB][hapmap]
rs6102936	0.82[CEU][hapmap]
rs6102937	0.88[GIH][hapmap];0.81[TSI][hapmap]
rs6102950	0.80[ASW][hapmap];0.88[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs6102951	0.88[CEU][hapmap]
rs6102952	0.88[CEU][hapmap]
rs6102953	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6102954	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6102957	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62203850	0.85[EUR][1000 genomes]
rs722556	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs73110421	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7360934	0.80[ASW][hapmap];0.83[CEU][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes]
rs7360961	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7361360	0.82[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7362850	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7362882	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7362883	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs761009	0.88[CEU][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap]
rs761010	0.88[CEU][hapmap]
rs8119203	0.82[CEU][hapmap]
rs8121443	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs874921	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs874922	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs874923	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs909862	0.80[ASW][hapmap];0.88[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs909863	0.88[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs909864	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9974028	0.83[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:55 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1055546	chr20:41102999-41260749	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1064253	chr20:41120425-41379706	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv586006	chr20:41157707-41290936	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1063513	chr20:41171076-41303205	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1056430	chr20:41171814-41243487	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv586009	chr20:41174105-41254693	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv870259	chr20:41174537-41251308	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv586011	chr20:41174693-41243236	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv912875	chr20:41174693-41254183	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv519654	chr20:41174693-41254693	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv912876	chr20:41174693-41296994	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv432118	chr20:41175615-41243286	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv586012	chr20:41176364-41243236	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1061179	chr20:41178700-41243024	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1057508	chr20:41178700-41243487	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv586013	chr20:41178858-41243236	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv586014	chr20:41178858-41252905	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv432119	chr20:41178886-41243286	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv915994	chr20:41180550-41464507	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv432120	chr20:41181486-41243186	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv586016	chr20:41182311-41243236	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv586017	chr20:41182311-41261444	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv526415	chr20:41184009-41290936	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv1063974	chr20:41185138-41292788	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv586018	chr20:41188318-41297693	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
27	nsv532517	chr20:41188651-41342196	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
28	nsv528161	chr20:41202935-41297693	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
29	nsv1055754	chr20:41205911-41243487	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
30	nsv1057302	chr20:41206845-41243487	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
31	nsv586019	chr20:41207365-41241888	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
32	nsv586020	chr20:41207365-41243236	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
33	nsv949644	chr20:41207365-41333541	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
34	nsv458979	chr20:41210746-41243236	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
35	nsv586021	chr20:41210746-41243236	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
36	nsv1066966	chr20:41211604-41272850	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
37	nsv1056856	chr20:41214474-41263409	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
38	nsv912878	chr20:41222480-41361424	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
39	nsv1067538	chr20:41225020-41284395	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
40	nsv1066761	chr20:41226302-41269430	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
41	nsv1055687	chr20:41227592-41284395	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
42	nsv833988	chr20:41227788-41379921	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
43	nsv432121	chr20:41228586-41277097	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
44	nsv458980	chr20:41228738-41284782	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
45	nsv586022	chr20:41228738-41284782	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
46	nsv586023	chr20:41228738-41297693	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
47	nsv912879	chr20:41229217-41285978	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
48	nsv432122	chr20:41230786-41281086	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
49	nsv1065268	chr20:41236087-41260749	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
50	nsv912880	chr20:41238504-41296994	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17841999	PTPRT	cis	cerebellum	SCAN
rs17841999	KIAA1755	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41240000-41242800	Enhancers	Fetal Muscle Leg	muscle
2	chr20:41240600-41242200	Enhancers	Fetal Brain Female	brain
3	chr20:41241000-41242200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr20:41241800-41242400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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