Variant report

Variant	rs12245742
Chromosome Location	chr10:5274116-5274117
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 162 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10795255	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs10795256	0.95[EUR][1000 genomes]
rs10904440	0.97[EUR][1000 genomes]
rs11253051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253052	1.00[CEU][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253053	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253054	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253057	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253059	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253060	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11253066	1.00[ASN][1000 genomes]
rs11253067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];1.00[ASN][1000 genomes]
rs11591916	1.00[ASN][1000 genomes]
rs11592046	1.00[ASN][1000 genomes]
rs11592833	1.00[ASN][1000 genomes]
rs11594520	1.00[CHB][hapmap]
rs11594521	1.00[ASN][1000 genomes]
rs11595029	0.83[ASN][1000 genomes]
rs11595482	1.00[ASN][1000 genomes]
rs11595920	1.00[ASN][1000 genomes]
rs11597152	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11597641	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11597812	1.00[ASN][1000 genomes]
rs11597910	1.00[ASN][1000 genomes]
rs11598244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11599367	0.83[ASN][1000 genomes]
rs11599875	1.00[ASN][1000 genomes]
rs11814640	1.00[ASN][1000 genomes]
rs12240608	1.00[ASN][1000 genomes]
rs12243692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12245676	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249368	1.00[ASN][1000 genomes]
rs12253074	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12253078	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12258997	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12260226	1.00[ASN][1000 genomes]
rs12265359	1.00[ASN][1000 genomes]
rs12265975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12266035	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12267307	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12784633	1.00[ASN][1000 genomes]
rs1334474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs1334475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1413624	0.92[EUR][1000 genomes]
rs1413781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs17134652	1.00[ASN][1000 genomes]
rs17134654	1.00[ASN][1000 genomes]
rs1889457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs1931671	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1931673	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1931676	1.00[ASN][1000 genomes]
rs1931677	1.00[ASN][1000 genomes]
rs2398152	1.00[ASN][1000 genomes]
rs2398184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2398185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895056	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34524110	1.00[ASN][1000 genomes]
rs34551905	1.00[ASN][1000 genomes]
rs34582570	1.00[ASN][1000 genomes]
rs34820657	1.00[ASN][1000 genomes]
rs34843899	1.00[ASN][1000 genomes]
rs34960702	1.00[ASN][1000 genomes]
rs35036396	1.00[ASN][1000 genomes]
rs35266926	1.00[ASN][1000 genomes]
rs35380685	1.00[ASN][1000 genomes]
rs35814115	1.00[ASN][1000 genomes]
rs35850551	1.00[ASN][1000 genomes]
rs35891495	1.00[ASN][1000 genomes]
rs35934477	1.00[ASN][1000 genomes]
rs3996537	1.00[ASN][1000 genomes]
rs4424568	1.00[ASN][1000 genomes]
rs4881412	1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs4881414	0.99[EUR][1000 genomes]
rs4881420	1.00[ASN][1000 genomes]
rs55644808	1.00[ASN][1000 genomes]
rs55661634	1.00[ASN][1000 genomes]
rs55743334	1.00[ASN][1000 genomes]
rs56080597	1.00[ASN][1000 genomes]
rs56095117	1.00[ASN][1000 genomes]
rs56107516	1.00[ASN][1000 genomes]
rs56138307	1.00[ASN][1000 genomes]
rs56211970	1.00[ASN][1000 genomes]
rs56223986	1.00[ASN][1000 genomes]
rs56264219	1.00[ASN][1000 genomes]
rs56347435	1.00[ASN][1000 genomes]
rs56403685	1.00[ASN][1000 genomes]
rs56409515	1.00[ASN][1000 genomes]
rs59227936	1.00[ASN][1000 genomes]
rs59389170	1.00[ASN][1000 genomes]
rs61690028	1.00[ASN][1000 genomes]
rs6601934	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66668806	1.00[ASN][1000 genomes]
rs67406543	1.00[ASN][1000 genomes]
rs67717827	1.00[ASN][1000 genomes]
rs7075810	1.00[ASN][1000 genomes]
rs7083175	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7087915	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7088228	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7095599	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7096360	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7096468	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7099476	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7099886	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7100445	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7100649	1.00[ASN][1000 genomes]
rs72774249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72774250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72774251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72774259	1.00[ASN][1000 genomes]
rs72774260	1.00[ASN][1000 genomes]
rs72774265	1.00[ASN][1000 genomes]
rs72774268	1.00[ASN][1000 genomes]
rs72774270	1.00[ASN][1000 genomes]
rs72774271	1.00[ASN][1000 genomes]
rs72774272	1.00[ASN][1000 genomes]
rs72774273	1.00[ASN][1000 genomes]
rs72774276	1.00[ASN][1000 genomes]
rs72774277	1.00[ASN][1000 genomes]
rs72774278	1.00[ASN][1000 genomes]
rs72774279	1.00[ASN][1000 genomes]
rs72774280	1.00[ASN][1000 genomes]
rs72774288	1.00[ASN][1000 genomes]
rs72774291	1.00[ASN][1000 genomes]
rs72774295	1.00[ASN][1000 genomes]
rs72774297	1.00[ASN][1000 genomes]
rs72774298	1.00[ASN][1000 genomes]
rs72774299	1.00[ASN][1000 genomes]
rs72774301	1.00[ASN][1000 genomes]
rs72774302	1.00[ASN][1000 genomes]
rs72778420	1.00[ASN][1000 genomes]
rs72778422	1.00[ASN][1000 genomes]
rs72778437	1.00[ASN][1000 genomes]
rs7896353	1.00[ASN][1000 genomes]
rs7903794	1.00[ASN][1000 genomes]
rs7904988	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv549883	chr10:5037926-5275762	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1036291	chr10:5076258-5456234	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv540472	chr10:5133561-5284334	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1048081	chr10:5149144-5321395	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv3387745	chr10:5201939-5324885	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	esv3370619	chr10:5201974-5324834	Enhancers Active TSS Weak transcription 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	10 gene(s)	inside rSNPs	diseases
13	esv3320807	chr10:5202006-5324760	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	esv3521675	chr10:5202012-5324815	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	esv3521676	chr10:5202012-5324815	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	esv3332233	chr10:5202023-5324788	ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv3405253	chr10:5202043-5324758	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	esv4943	chr10:5202052-5324829	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	esv3320818	chr10:5202105-5324796	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	nsv932104	chr10:5203626-5641023	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
21	nsv549886	chr10:5205437-5632060	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
22	nsv1054865	chr10:5225305-5638119	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
23	nsv5643	chr10:5229780-5302665	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
24	nsv508566	chr10:5256836-5321354	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv549887	chr10:5263628-5303742	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12245742	IL2RA	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5264200-5275600	Weak transcription	A549	lung
2	chr10:5271200-5276600	Weak transcription	Gastric	stomach

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