Variant report

Variant	rs4242893
Chromosome Location	chr12:8630929-8630930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:8625872..8627990-chr12:8629712..8631446,2	K562	blood:

Extended variants
information (count: 140 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10734709	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10734713	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10743393	1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10743396	1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10770692	1.00[ASN][1000 genomes]
rs10770711	0.81[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10770722	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10770723	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10770734	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10770735	1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10770736	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10770737	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10770738	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10770739	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10770740	0.83[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10770775	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770776	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10770793	0.83[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	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045652	0.98[EUR][1000 genomes]
rs11045708	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045757	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11045810	0.83[EUR][1000 genomes]
rs11045914	1.00[ASN][1000 genomes]
rs11829089	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12300621	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12302015	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12302854	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304190	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308954	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322968	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370044	1.00[ASN][1000 genomes]
rs12423976	0.98[EUR][1000 genomes]
rs4242888	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4242889	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242890	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs4242891	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242892	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242895	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4255605	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4258429	0.98[EUR][1000 genomes]
rs4264222	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4268555	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4296104	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4303299	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4326877	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4329732	1.00[CEU][hapmap]
rs4334073	0.93[CEU][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4343097	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4384442	1.00[ASN][1000 genomes]
rs4387429	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4388969	0.84[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4402377	0.88[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4420348	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4420349	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4420350	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4427631	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435079	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4445713	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4447245	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457803	0.92[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4460883	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4477485	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4486678	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520670	1.00[ASN][1000 genomes]
rs4528410	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4565980	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4576903	1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4616119	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4622339	0.84[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4623977	0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4623978	1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4625553	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4628756	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4638374	0.83[ASW][hapmap];0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4640002	0.83[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4641551	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4882942	0.82[CEU][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4882949	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882950	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882951	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883145	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4883146	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4883148	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4883149	0.84[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4883154	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883157	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs4883164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6487136	0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];1.00[ASN][1000 genomes]
rs7132871	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134303	1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302011	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302950	1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7304092	1.00[ASN][1000 genomes]
rs7306661	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7309596	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311079	0.82[EUR][1000 genomes]
rs7312356	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7312686	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312713	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315590	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315873	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962791	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963053	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964875	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968198	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7969317	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7969325	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7976692	0.99[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7976958	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977465	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7978179	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978218	0.98[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4242893	GABARAPL1	cis	parietal	SCAN
rs4242893	NANOGNB	cis	cerebellum	SCAN
rs4242893	CLEC12A	cis	parietal	SCAN
rs4242893	CLEC6A	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8628000-8638200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:8628400-8637400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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