Variant report

Variant	rs10863114
Chromosome Location	chr12:86332325-86332326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10082857	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10779220	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863094	0.83[ASN][1000 genomes]
rs10863111	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863112	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863113	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10863121	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10863124	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863146	0.81[TSI][hapmap]
rs11117089	0.83[ASN][1000 genomes]
rs11117115	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11117118	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11117122	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11117124	1.00[ASN][1000 genomes]
rs11117129	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11117146	0.81[TSI][hapmap]
rs11608539	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11611607	1.00[ASN][1000 genomes]
rs11615948	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs12313658	0.92[CEU][hapmap]
rs12369468	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12370270	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1349063	0.80[CEU][hapmap]
rs17354637	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897186	0.83[ASN][1000 genomes]
rs4143239	0.83[ASN][1000 genomes]
rs4919774	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61929393	1.00[ASN][1000 genomes]
rs61929394	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61929395	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61929399	0.83[ASN][1000 genomes]
rs61929421	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61929424	0.83[ASN][1000 genomes]
rs61930913	0.83[ASN][1000 genomes]
rs6539935	0.81[TSI][hapmap]
rs7132262	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7135154	0.83[ASN][1000 genomes]
rs7303256	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305869	0.81[TSI][hapmap]
rs7313373	0.81[TSI][hapmap]
rs7313442	0.81[TSI][hapmap]
rs7314272	0.81[TSI][hapmap]
rs73176252	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73177142	0.83[ASN][1000 genomes]
rs73177167	0.92[ASN][1000 genomes]
rs73177169	0.92[ASN][1000 genomes]
rs73177179	1.00[ASN][1000 genomes]
rs7397730	0.81[TSI][hapmap]
rs7966131	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966352	0.81[TSI][hapmap]
rs7972773	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973694	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975310	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975457	0.83[TSI][hapmap]
rs7976573	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9651977	1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv1797806	chr12:86198935-86425608	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv559667	chr12:86318004-86416212	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10863114	MGAT4C	cis	Thyroid	GTEx
rs10863114	RASSF9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86332000-86338200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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