Variant report

Variant	rs3850509
Chromosome Location	chr11:4980792-4980793
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	11:4789513-4794705..11:4979189-4988077	K562	blood:
2	11:4778081-4789138..11:4979189-4988077	K562	blood:

Variant related genes	Relation type
ENSG00000167346	Chromatin interaction
ENSG00000188069	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10837027	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12805257	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12805938	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2570573	0.86[CEU][hapmap]
rs2595988	0.86[CEU][hapmap]
rs2595993	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs2596002	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs3850508	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3906665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131097	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs840713	0.82[CEU][hapmap];0.82[GIH][hapmap]

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	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	esv2758254	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv2759799	chr11:4907893-5135331	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv7652	chr11:4946245-4997769	Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
5	nsv1054610	chr11:4953844-5004203	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
6	nsv526998	chr11:4954607-5074301	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1045154	chr11:4958462-5032685	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv540937	chr11:4958462-5032685	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1046693	chr11:4958462-5177455	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
10	nsv540938	chr11:4958462-5177455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
11	nsv64	chr11:4959236-4985373	Enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv896918	chr11:4960032-5001570	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
13	nsv1043799	chr11:4961506-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	nsv1046196	chr11:4961506-4995448	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
15	esv2760169	chr11:4961518-5233821	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
16	esv2757419	chr11:4961913-4992282	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
17	nsv1039389	chr11:4962632-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
18	nsv1054521	chr11:4962933-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
19	nsv1037087	chr11:4963707-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
20	nsv1050888	chr11:4964103-4987007	Enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
21	nsv1052561	chr11:4967061-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
22	nsv1039806	chr11:4967061-4995989	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
23	nsv1041662	chr11:4967061-5001831	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
24	nsv1041643	chr11:4967364-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
25	esv2760399	chr11:4967376-4987007	Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
26	nsv1049584	chr11:4968117-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
27	nsv1043954	chr11:4968117-4991090	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
28	nsv1046955	chr11:4968117-4992501	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
29	nsv1051927	chr11:4968117-4994984	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
30	nsv1053877	chr11:4968117-4995989	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
31	nsv553202	chr11:4968198-4995686	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
32	nsv1047492	chr11:4970231-4982916	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
33	nsv1053139	chr11:4970231-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
34	nsv1039964	chr11:4970231-4987007	Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
35	nsv1044638	chr11:4970231-4991090	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
36	nsv1050416	chr11:4970265-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
37	nsv1035589	chr11:4970331-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
38	nsv1043164	chr11:4971993-4983161	Inactive region	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
39	nsv1041826	chr11:4971993-4987007	Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
40	nsv1037674	chr11:4971993-4991090	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
41	nsv1052406	chr11:4971993-4994314	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
42	nsv1043366	chr11:4971993-4995989	Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
43	nsv1045940	chr11:4973083-4987007	Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3850509	OR51G2	cis	cerebellum	SCAN
rs3850509	OR52N1	cis	cerebellum	SCAN
rs3850509	OR56A5	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links