Variant report

Variant	rs2452808
Chromosome Location	chr12:86644744-86644745
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10776954	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10776958	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10776960	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10776967	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10858409	0.86[EUR][1000 genomes]
rs10858411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10858412	0.88[CEU][hapmap]
rs10858417	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10858420	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10858424	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1097997	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs11103946	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11117189	1.00[CHB][hapmap]
rs12372566	1.00[CHB][hapmap]
rs1389292	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1389294	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1389295	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs1463750	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1493413	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1493414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493417	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1493418	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1493419	0.83[CEU][hapmap]
rs1493420	0.81[AMR][1000 genomes]
rs1532263	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1628799	0.94[CEU][hapmap]
rs1689364	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs1698757	1.00[CHB][hapmap]
rs1994863	0.87[EUR][1000 genomes]
rs2178748	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2250915	0.81[AMR][1000 genomes]
rs2405932	0.82[CEU][hapmap]
rs2405934	0.88[CEU][hapmap]
rs2406120	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406121	0.92[EUR][1000 genomes]
rs2406128	0.89[CEU][hapmap]
rs2452803	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2452805	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2465142	0.89[EUR][1000 genomes]
rs2465145	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2465148	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2471562	0.81[AMR][1000 genomes]
rs2471565	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2471567	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs2897269	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs2897273	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4329741	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6538021	0.83[CEU][hapmap]
rs6538023	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs6538027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7134045	0.82[CEU][hapmap]
rs7134944	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7303642	0.92[EUR][1000 genomes]
rs7309839	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs7312245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7953494	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7954833	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963957	0.86[EUR][1000 genomes]
rs7966656	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972185	0.94[CEU][hapmap]
rs7975314	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs839099	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs839100	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs839106	1.00[CHB][hapmap]
rs839107	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs839109	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs839112	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs839113	1.00[CHB][hapmap]
rs839114	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs839115	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs839116	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs839117	0.84[CEU][hapmap]
rs839119	1.00[CHB][hapmap]
rs839120	1.00[CHB][hapmap]
rs839124	1.00[CHB][hapmap]
rs839128	1.00[CHB][hapmap]
rs839134	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs839138	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs839139	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs839147	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs839162	0.88[CEU][hapmap]
rs839183	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs839189	1.00[CHB][hapmap]
rs839191	1.00[CHB][hapmap]
rs844433	0.94[CEU][hapmap]
rs844437	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs858213	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs866893	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1053087	chr12:86569126-86733418	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541564	chr12:86569126-86733418	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1037003	chr12:86610040-86798121	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1045386	chr12:86616015-86733418	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv541565	chr12:86616015-86733418	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2452808	MGAT4C	cis	Heart Left Ventricle	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86643400-86646600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:86643800-86648000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:86644000-86650000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr12:86644200-86655400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:86644400-86647400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:86644600-86645000	Weak transcription	Fetal Heart	heart

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