Variant report

Variant	rs6102929
Chromosome Location	chr20:41230763-41230764
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1013030	0.84[CEU][hapmap]
rs10854226	0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs1157668	0.89[JPT][hapmap]
rs13038923	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs13039393	0.84[CEU][hapmap]
rs13045128	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs13045132	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs17841999	0.88[CHB][hapmap]
rs1883842	0.84[CEU][hapmap]
rs1883843	1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs2223542	0.82[MEX][hapmap]
rs2903589	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs34027202	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35952939	0.88[ASN][1000 genomes]
rs56946934	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6016854	0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs6016855	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs6016858	0.85[ASN][1000 genomes]
rs6030350	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6030351	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6030352	0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs6030355	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6030356	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6030358	0.91[EUR][1000 genomes]
rs6030359	0.91[EUR][1000 genomes]
rs6030376	0.83[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap]
rs6030381	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs6030384	0.88[CHB][hapmap]
rs6030385	0.88[CHB][hapmap]
rs6093681	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs6093685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6093689	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6093690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6093692	0.90[EUR][1000 genomes]
rs6093693	0.92[CEU][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs6093694	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6093695	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6093697	0.92[CEU][hapmap];0.95[GIH][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs6093705	0.83[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs6102918	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6102922	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6102925	0.86[CHD][hapmap]
rs6102928	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6102933	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6102967	0.89[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs722556	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7274157	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs7274201	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs761010	0.89[JPT][hapmap]
rs8114527	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs8114592	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs8114928	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs8114932	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs8121332	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs8124013	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs997893	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:52 , 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	nsv458978	chr20:41174693-41230763	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv586010	chr20:41174693-41230763	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	nsv1065411	chr20:41181079-41234914	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	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
25	nsv586015	chr20:41182311-41240700	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
26	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
27	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
28	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
29	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
30	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
31	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
32	nsv1062850	chr20:41202830-41239845	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
33	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
34	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
35	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
36	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
37	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
38	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
39	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
40	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
41	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
42	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
43	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
44	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
45	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
46	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
47	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
48	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
49	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
50	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6102929	SNORA71B	cis	cerebellum	SCAN
rs6102929	R3HDML	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41219200-41240200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:41226200-41232400	Weak transcription	Pancreas	Pancrea
3	chr20:41228000-41231200	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links