Variant report

Variant	rs7954883
Chromosome Location	chr12:86888917-86888918
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10745415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10745421	1.00[CHB][hapmap];0.88[GIH][hapmap]
rs10776958	0.82[EUR][1000 genomes]
rs10776967	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776975	1.00[YRI][hapmap]
rs10858411	1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs10858417	0.82[EUR][1000 genomes]
rs10858420	1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10858421	1.00[YRI][hapmap]
rs10858424	1.00[CHB][hapmap]
rs10858429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11103946	0.84[EUR][1000 genomes]
rs12372566	1.00[CHB][hapmap]
rs1922745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178748	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap]
rs2406142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2897269	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs2897273	1.00[CHB][hapmap];0.80[MEX][hapmap];0.88[MKK][hapmap]
rs4300451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351884	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4370997	0.92[CEU][hapmap]
rs4444151	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4612887	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4842512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6538040	1.00[CHB][hapmap]
rs6538043	0.83[CEU][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6538044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134944	1.00[CHB][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap]
rs7302391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs7309839	1.00[CHB][hapmap]
rs7316265	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7954833	1.00[CHB][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967529	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7975314	0.82[ASW][hapmap];1.00[CHB][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754127	chr12:86723232-87576932	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv899395	chr12:86813367-87177972	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv916862	chr12:86837694-87718558	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv899396	chr12:86863041-87276957	ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv899397	chr12:86863041-87636831	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv899398	chr12:86880442-87051310	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv899399	chr12:86880442-87177972	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv275003	chr12:86880778-86890003	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7954883	MGAT4C	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86888600-86890000	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr12:86888800-86889400	Enhancers	HUES48 Cell Line	embryonic stem cell

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