Variant report

Variant	rs12476739
Chromosome Location	chr2:52746669-52746670
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11125431	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12373684	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12463745	0.91[AFR][1000 genomes]
rs12463812	0.89[AFR][1000 genomes]
rs12464625	0.91[AFR][1000 genomes]
rs12467293	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12467957	0.88[AFR][1000 genomes]
rs12468004	0.91[EUR][1000 genomes]
rs12469108	0.80[ASN][1000 genomes]
rs12469137	0.80[ASN][1000 genomes]
rs12471695	0.91[AFR][1000 genomes]
rs12472349	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12475183	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12475393	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12475455	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12475601	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12476788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405359	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568988	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17043074	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17043076	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17043080	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17043082	0.81[ASN][1000 genomes]
rs17043083	0.81[ASN][1000 genomes]
rs17043086	0.80[ASN][1000 genomes]
rs36031897	0.81[ASN][1000 genomes]
rs4334531	0.81[EUR][1000 genomes]
rs57001563	0.80[ASN][1000 genomes]
rs57381756	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57766683	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58387633	0.90[AFR][1000 genomes]
rs58479536	0.91[AFR][1000 genomes]
rs58520233	0.80[ASN][1000 genomes]
rs59711478	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59727652	0.91[AFR][1000 genomes]
rs59751172	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59834823	0.91[AFR][1000 genomes]
rs60669340	0.81[ASN][1000 genomes]
rs60870297	0.80[ASN][1000 genomes]
rs6545286	0.83[ASN][1000 genomes]
rs6545287	0.83[ASN][1000 genomes]
rs6545288	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6715457	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716737	0.90[AFR][1000 genomes]
rs6749593	0.83[ASN][1000 genomes]
rs72882636	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72882642	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72882646	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72882649	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72884204	0.86[AMR][1000 genomes]
rs72892992	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72893002	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72894810	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72894833	0.91[AFR][1000 genomes]
rs72894838	0.91[AFR][1000 genomes]
rs7557580	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557874	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570162	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570257	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596696	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9309231	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:64 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009513	chr2:51890060-52821980	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1007633	chr2:52217555-52862389	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv535714	chr2:52217555-52862389	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv874111	chr2:52383698-52962055	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1014619	chr2:52496317-52821980	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv535717	chr2:52496317-52821980	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv998227	chr2:52527889-52821980	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv581929	chr2:52599360-52761239	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv2760562	chr2:52681203-52781542	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1831158	chr2:52692840-52785972	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	esv2754871	chr2:52695749-52922949	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv533591	chr2:52706226-52781440	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv874124	chr2:52706489-52760453	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv997314	chr2:52720976-52781530	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv999698	chr2:52720976-52851561	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	esv1826326	chr2:52724060-52785181	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv2728	chr2:52725177-52807896	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv834036	chr2:52727240-52916200	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	esv2757797	chr2:52727380-52814537	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv2759049	chr2:52727380-52814537	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv1005206	chr2:52731518-52781530	Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv1002290	chr2:52735148-52781530	Enhancers Weak transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
23	nsv874125	chr2:52735368-52851073	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv1008360	chr2:52736181-52781530	Weak transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
25	nsv1011241	chr2:52736181-52794130	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv1008762	chr2:52736614-52758929	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
27	nsv1003817	chr2:52736614-52781530	Weak transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
28	nsv1007065	chr2:52736765-52759103	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
29	nsv1014974	chr2:52736765-52781530	Weak transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
30	nsv1011879	chr2:52737183-52759103	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
31	nsv998171	chr2:52737183-52781530	Enhancers Weak transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
32	nsv1007294	chr2:52737183-52794130	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
33	nsv581931	chr2:52737658-52797840	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
34	nsv999531	chr2:52738012-52759103	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
35	nsv1008652	chr2:52738012-52781530	Weak transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
36	nsv1009301	chr2:52738012-52794130	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
37	esv1833224	chr2:52738716-52783773	Weak transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
38	nsv1014337	chr2:52739028-52759103	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
39	nsv1003100	chr2:52739028-52781530	Weak transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
40	esv1800225	chr2:52739028-52790493	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
41	esv2755042	chr2:52739102-52883790	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
42	nsv1006282	chr2:52739168-52781530	Enhancers ZNF genes & repeats Weak transcription	lncRNA	n/a	inside rSNPs	diseases
43	esv3584758	chr2:52739180-52792828	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
44	nsv1004419	chr2:52741737-52765682	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
45	nsv999461	chr2:52741737-52781179	Enhancers Weak transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
46	nsv1012767	chr2:52741737-52781283	Weak transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
47	nsv1009737	chr2:52741737-52781530	Weak transcription Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
48	nsv581932	chr2:52741737-52785181	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
49	esv1821464	chr2:52741737-52785554	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
50	nsv1003407	chr2:52743925-52765682	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52746400-52746800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:52746600-52746800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr2:52746600-52747600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:52746600-52748400	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links