Variant report

Variant	rs2223542
Chromosome Location	chr20:41277097-41277098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1157668	0.90[CHB][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13040760	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17810239	0.80[CEU][hapmap];0.89[GIH][hapmap]
rs2223541	0.82[JPT][hapmap]
rs2867490	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2903589	0.81[CHB][hapmap]
rs6016852	0.80[CEU][hapmap];0.89[GIH][hapmap]
rs6016854	0.82[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6016855	0.88[CEU][hapmap];0.94[GIH][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs6016856	0.89[GIH][hapmap];0.86[AMR][1000 genomes]
rs6016858	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6030376	0.88[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes]
rs6030380	0.80[CEU][hapmap];0.89[GIH][hapmap]
rs6030381	0.82[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs6093705	0.82[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs6102929	0.82[MEX][hapmap]
rs6102967	0.84[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs761010	0.90[CHB][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs997893	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:49 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	nsv912880	chr20:41238504-41296994	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv458981	chr20:41240700-41290936	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv586024	chr20:41240700-41290936	Enhancers ZNF genes & repeats Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv912881	chr20:41240700-41296994	Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv912882	chr20:41240700-41296994	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv1057771	chr20:41241208-41287845	Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv912885	chr20:41243236-41284395	Enhancers Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv912886	chr20:41243236-41296994	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv912887	chr20:41243236-41296994	Enhancers Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	nsv912888	chr20:41243236-41302843	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	esv2756739	chr20:41252905-41277097	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
33	esv2758795	chr20:41252905-41277097	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
34	esv2754684	chr20:41253081-41281104	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
35	esv2760672	chr20:41253498-41279219	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv586025	chr20:41254183-41278325	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
37	nsv817896	chr20:41254693-41278325	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
38	nsv1060248	chr20:41255601-41277097	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
39	esv2752939	chr20:41255613-41277097	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
40	nsv432126	chr20:41255613-41282426	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
41	nsv1065159	chr20:41255777-41277097	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
42	esv3693292	chr20:41257456-41278325	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
43	nsv517647	chr20:41257456-41278325	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
44	nsv586026	chr20:41261444-41297693	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
45	esv2830283	chr20:41266942-41290936	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
46	nsv470552	chr20:41269321-41297693	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
47	nsv458982	chr20:41269321-41302843	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
48	nsv586027	chr20:41269321-41302843	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
49	nsv522445	chr20:41273663-41280315	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2223542	SEMG1	cis	parietal	SCAN
rs2223542	ACTR5	cis	cerebellum	SCAN
rs2223542	SNORA71B	cis	cerebellum	SCAN
rs2223542	KIAA1755	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41271600-41300800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:41277000-41277400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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