Variant report

Variant	rs61920546
Chromosome Location	chr12:8601281-8601282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 148 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10734709	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734713	1.00[ASN][1000 genomes]
rs10743393	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743396	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770692	1.00[ASN][1000 genomes]
rs10770711	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770722	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770723	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770734	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770735	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770736	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770737	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770738	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770739	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770740	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770775	1.00[ASN][1000 genomes]
rs10770776	1.00[ASN][1000 genomes]
rs10770793	1.00[ASN][1000 genomes]
rs10841590	1.00[ASN][1000 genomes]
rs10841595	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045398	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045427	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045643	1.00[ASN][1000 genomes]
rs11045708	1.00[ASN][1000 genomes]
rs11045757	1.00[ASN][1000 genomes]
rs11045914	1.00[ASN][1000 genomes]
rs11829089	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300621	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302015	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302854	1.00[ASN][1000 genomes]
rs12304190	1.00[ASN][1000 genomes]
rs12308954	1.00[ASN][1000 genomes]
rs12322968	1.00[ASN][1000 genomes]
rs12370044	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242888	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242889	1.00[ASN][1000 genomes]
rs4242891	1.00[ASN][1000 genomes]
rs4242892	1.00[ASN][1000 genomes]
rs4242893	1.00[ASN][1000 genomes]
rs4255605	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264222	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4268555	1.00[ASN][1000 genomes]
rs4296104	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4326877	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334073	1.00[ASN][1000 genomes]
rs4343097	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4384442	1.00[ASN][1000 genomes]
rs4387429	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4388969	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4402377	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420348	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420349	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420350	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427631	1.00[ASN][1000 genomes]
rs4435079	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447245	1.00[ASN][1000 genomes]
rs4460883	1.00[ASN][1000 genomes]
rs4477485	1.00[ASN][1000 genomes]
rs4486678	1.00[ASN][1000 genomes]
rs4497482	0.86[EUR][1000 genomes]
rs4520670	1.00[ASN][1000 genomes]
rs4528410	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4565980	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4576903	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616119	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622339	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4623977	0.90[EUR][1000 genomes]
rs4623978	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4625553	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4628756	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638374	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640002	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4641551	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882942	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882949	1.00[ASN][1000 genomes]
rs4882950	1.00[ASN][1000 genomes]
rs4882951	1.00[ASN][1000 genomes]
rs4883145	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883146	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883148	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883149	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883154	1.00[ASN][1000 genomes]
rs4883164	1.00[ASN][1000 genomes]
rs57529938	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58537563	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60630733	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61920533	0.87[AFR][1000 genomes]
rs61920534	0.83[AFR][1000 genomes]
rs61920535	0.88[AFR][1000 genomes]
rs61920536	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61920537	1.00[ASN][1000 genomes]
rs61920538	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61920539	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61920540	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61920541	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61920543	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6487135	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487136	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132871	1.00[ASN][1000 genomes]
rs7134303	1.00[ASN][1000 genomes]
rs7302011	1.00[ASN][1000 genomes]
rs7302950	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304092	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306661	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309596	1.00[ASN][1000 genomes]
rs7312356	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312686	1.00[ASN][1000 genomes]
rs7312713	1.00[ASN][1000 genomes]
rs7315590	1.00[ASN][1000 genomes]
rs7315873	1.00[ASN][1000 genomes]
rs7962791	1.00[ASN][1000 genomes]
rs7963053	1.00[ASN][1000 genomes]
rs7964875	1.00[ASN][1000 genomes]
rs7968198	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969317	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969325	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7976958	1.00[ASN][1000 genomes]
rs7978179	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048545	chr12:7778760-8608231	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv541368	chr12:7778760-8608231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
4	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	93 gene(s)	inside rSNPs	diseases
5	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv916941	chr12:8003501-8608220	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
7	nsv1040302	chr12:8245364-8695612	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv541397	chr12:8245364-8695612	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv427902	chr12:8276546-8623987	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv1036525	chr12:8317823-8603777	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv973015	chr12:8371568-8602961	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv1046231	chr12:8401834-8603777	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv1042364	chr12:8417967-8605829	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv1044543	chr12:8449100-8792569	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
15	nsv508664	chr12:8450876-8604691	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv898736	chr12:8479342-8605216	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv1039504	chr12:8494944-8780137	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	esv1809025	chr12:8511575-8607833	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv1047915	chr12:8536600-8603777	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv598	chr12:8542677-8603512	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
21	esv17877	chr12:8544884-8601829	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv821277	chr12:8544884-8601829	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv1052842	chr12:8554391-8601982	Enhancers Weak transcription Active TSS Strong transcription	TF binding region CpG island	6 gene(s)	inside rSNPs	diseases
24	nsv1041244	chr12:8556681-8601982	Active TSS Weak transcription Enhancers Strong transcription	TF binding region CpG island	5 gene(s)	inside rSNPs	diseases
25	nsv1049919	chr12:8558476-8601982	Active TSS Weak transcription Enhancers Strong transcription	TF binding region CpG island	5 gene(s)	inside rSNPs	diseases
26	nsv1045748	chr12:8558476-8602354	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island	5 gene(s)	inside rSNPs	diseases
27	nsv1045232	chr12:8558476-8602970	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island	5 gene(s)	inside rSNPs	diseases
28	nsv1047840	chr12:8558476-8603777	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island	6 gene(s)	inside rSNPs	diseases
29	nsv1050975	chr12:8559093-8603777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription	TF binding region CpG island	6 gene(s)	inside rSNPs	diseases
30	nsv557342	chr12:8599397-8774527	Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61920546	CLEC6A	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8594400-8603400	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr12:8594600-8601800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr12:8601000-8602200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:8601000-8602200	Active TSS	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links