Variant report

Variant	rs1999435
Chromosome Location	chr9:1513849-1513850
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10961808	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10961872	0.97[ASN][1000 genomes]
rs10961888	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1331988	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1339490	0.97[ASN][1000 genomes]
rs1339491	0.97[ASN][1000 genomes]
rs1576747	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2050757	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183842	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4574900	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4741437	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4741438	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5023161	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56958352	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60028299	0.97[ASN][1000 genomes]
rs9298725	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9918936	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:43 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016321	chr9:1034594-1592366	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv539908	chr9:1034594-1592366	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2758176	chr9:1055347-1529128	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2759656	chr9:1055347-1529128	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2752273	chr9:1062218-1824888	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1026043	chr9:1079462-1732502	Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv539909	chr9:1079462-1732502	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv613052	chr9:1311310-1662585	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1031422	chr9:1318383-1716944	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv539912	chr9:1318383-1716944	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1032384	chr9:1320386-1719409	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv539913	chr9:1320386-1719409	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1026875	chr9:1429839-1554752	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv539915	chr9:1429839-1554752	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1018321	chr9:1444746-1556848	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
17	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
18	nsv1030848	chr9:1466368-1675561	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	esv2756453	chr9:1469726-1521527	Enhancers Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv1017054	chr9:1470288-1554752	Weak transcription Enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv1017016	chr9:1483886-1575368	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv539918	chr9:1483886-1575368	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv1024615	chr9:1490371-1521263	Enhancers Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv892032	chr9:1491213-1538884	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv1031845	chr9:1492361-1554752	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv1024274	chr9:1496424-1514379	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv1025222	chr9:1497943-1518792	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
28	nsv1024603	chr9:1499410-1575368	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv539919	chr9:1499410-1575368	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv522460	chr9:1499641-1513917	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv466066	chr9:1499641-1513917	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
32	nsv613070	chr9:1499641-1513917	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv613071	chr9:1499641-1515481	Enhancers Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
34	nsv613072	chr9:1499641-1516528	Enhancers Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv1033521	chr9:1500317-1514379	Enhancers Strong transcription Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
36	nsv429981	chr9:1500755-1513917	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
37	nsv613073	chr9:1501977-1513917	Enhancers Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
38	nsv892033	chr9:1501977-1567276	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
39	nsv613074	chr9:1503556-1513849	Enhancers Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
40	nsv437641	chr9:1503647-1516692	Enhancers Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases
41	nsv1030166	chr9:1504955-1540499	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
42	nsv1028284	chr9:1505457-1540499	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
43	nsv438088	chr9:1510299-1526383	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1999435	RFX3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:1512800-1514200	Enhancers	NHEK	skin
2	chr9:1513200-1514000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:1513400-1514800	Enhancers	Fetal Muscle Leg	muscle
4	chr9:1513800-1514600	Enhancers	Adipose Nuclei	Adipose

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