Variant report

Variant	rs4268555
Chromosome Location	chr12:8646485-8646486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 140 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10734709	1.00[ASN][1000 genomes]
rs10734713	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743393	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10743396	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10770692	1.00[ASN][1000 genomes]
rs10770711	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10770722	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10770723	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10770734	1.00[ASN][1000 genomes]
rs10770735	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10770736	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10770737	1.00[ASN][1000 genomes]
rs10770738	1.00[ASN][1000 genomes]
rs10770739	1.00[ASN][1000 genomes]
rs10770740	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10770775	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770776	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770793	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841590	1.00[ASN][1000 genomes]
rs10841595	1.00[ASN][1000 genomes]
rs11045398	1.00[ASN][1000 genomes]
rs11045427	1.00[ASN][1000 genomes]
rs11045643	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045652	0.84[EUR][1000 genomes]
rs11045708	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045757	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045810	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11045914	1.00[ASN][1000 genomes]
rs11829089	1.00[ASN][1000 genomes]
rs12300621	1.00[ASN][1000 genomes]
rs12302015	1.00[ASN][1000 genomes]
rs12302854	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304190	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308954	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322968	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370044	1.00[ASN][1000 genomes]
rs12423976	0.84[EUR][1000 genomes]
rs4242888	1.00[ASN][1000 genomes]
rs4242889	1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242890	1.00[JPT][hapmap]
rs4242891	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242892	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242893	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242895	0.84[EUR][1000 genomes]
rs4255605	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4258429	0.84[EUR][1000 genomes]
rs4264222	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4296104	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4303299	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4326877	1.00[ASN][1000 genomes]
rs4329732	0.89[CEU][hapmap]
rs4334073	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343097	1.00[ASN][1000 genomes]
rs4384442	1.00[ASN][1000 genomes]
rs4387429	1.00[ASN][1000 genomes]
rs4388969	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4402377	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4420348	1.00[ASN][1000 genomes]
rs4420349	1.00[ASN][1000 genomes]
rs4420350	1.00[ASN][1000 genomes]
rs4427631	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435079	1.00[ASN][1000 genomes]
rs4445713	0.82[AMR][1000 genomes]
rs4447245	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457803	0.84[EUR][1000 genomes]
rs4460883	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4477485	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486678	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520670	1.00[ASN][1000 genomes]
rs4528410	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4565980	1.00[ASN][1000 genomes]
rs4576903	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4616119	1.00[ASN][1000 genomes]
rs4622339	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4623978	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4625553	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4628756	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4638374	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4640002	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4641551	1.00[ASN][1000 genomes]
rs4882942	1.00[ASN][1000 genomes]
rs4882949	0.89[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882950	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882951	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883145	1.00[ASN][1000 genomes]
rs4883146	1.00[ASN][1000 genomes]
rs4883148	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4883149	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4883154	1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883157	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs4883164	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883165	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57529938	1.00[ASN][1000 genomes]
rs58537563	1.00[ASN][1000 genomes]
rs60630733	1.00[ASN][1000 genomes]
rs61920536	1.00[ASN][1000 genomes]
rs61920537	1.00[ASN][1000 genomes]
rs61920538	1.00[ASN][1000 genomes]
rs61920539	1.00[ASN][1000 genomes]
rs61920540	1.00[ASN][1000 genomes]
rs61920541	1.00[ASN][1000 genomes]
rs61920543	1.00[ASN][1000 genomes]
rs61920546	1.00[ASN][1000 genomes]
rs6487135	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6487136	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6487209	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7132871	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134303	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302011	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302950	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7304092	1.00[ASN][1000 genomes]
rs7306661	1.00[ASN][1000 genomes]
rs7309596	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311079	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7312356	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7312686	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312713	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315590	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315873	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962791	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963053	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964875	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968198	1.00[ASN][1000 genomes]
rs7969317	1.00[ASN][1000 genomes]
rs7969325	1.00[ASN][1000 genomes]
rs7976692	0.84[EUR][1000 genomes]
rs7976958	0.89[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978179	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978218	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv933050	chr12:8602789-8775989	Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv518772	chr12:8615809-8667579	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv518125	chr12:8615809-8671274	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1035270	chr12:8619562-8674062	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv933555	chr12:8627165-8775989	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	8 gene(s)	inside rSNPs	diseases
11	nsv933639	chr12:8627243-8775989	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4268555	CLEC12A	cis	parietal	SCAN
rs4268555	ATN1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8643000-8649000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:8644000-8646800	Enhancers	Primary hematopoietic stem cells	blood
3	chr12:8644400-8646800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:8644600-8646600	Enhancers	Primary B cells from cord blood	blood
5	chr12:8644600-8646800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr12:8645000-8646600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:8645000-8646800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:8645200-8646600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:8645200-8646600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:8645200-8646800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:8645600-8646600	Flanking Active TSS	GM12878-XiMat	blood
12	chr12:8645800-8646800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr12:8646200-8646800	Enhancers	Fetal Thymus	thymus
14	chr12:8646400-8646800	Enhancers	Primary T cells from cord blood	blood

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