Variant report

Variant	rs1354258
Chromosome Location	chr12:86485647-86485648
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10746359	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10779224	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10779225	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10779227	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10779231	0.83[CEU][hapmap]
rs10779236	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10863139	1.00[CHB][hapmap]
rs10863141	1.00[CHB][hapmap]
rs10863146	0.81[CEU][hapmap]
rs10863149	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10863162	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863164	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11117146	0.81[CEU][hapmap]
rs11117148	1.00[CHB][hapmap]
rs11117152	1.00[CHB][hapmap]
rs11117154	1.00[CHB][hapmap]
rs11513955	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11513957	0.81[CEU][hapmap]
rs11614214	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12298516	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12301701	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1393612	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1493407	0.82[JPT][hapmap]
rs1502799	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1502800	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502803	1.00[CHB][hapmap]
rs6539935	0.81[CEU][hapmap]
rs6539941	0.81[ASN][1000 genomes]
rs6539942	0.88[CEU][hapmap];0.81[ASN][1000 genomes]
rs7294859	1.00[CHB][hapmap]
rs7301280	0.82[CEU][hapmap]
rs7302043	1.00[CHB][hapmap]
rs7305869	0.81[CEU][hapmap]
rs7313373	0.81[CEU][hapmap]
rs7313442	0.81[CEU][hapmap]
rs7314272	0.81[CEU][hapmap]
rs7398950	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7485285	1.00[CEU][hapmap]
rs7485853	1.00[CHB][hapmap]
rs7489114	1.00[CHB][hapmap]
rs7965726	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7967417	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs7975457	0.81[CEU][hapmap]
rs7978562	0.81[CEU][hapmap]
rs8181635	1.00[CEU][hapmap]
rs839091	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs839135	0.82[JPT][hapmap]
rs865720	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs952851	1.00[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9669353	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9706029	1.00[CHB][hapmap]
rs9738989	1.00[CHB][hapmap]
rs9804820	1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv832476	chr12:86389751-86497122	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	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
4	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
5	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
6	esv3345033	chr12:86458294-86514745	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv470311	chr12:86484366-86550783	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1354258	MGAT4C	cis	Nerve Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86484400-86486000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:86485000-86486000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:86485200-86485800	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr12:86485200-86486000	Enhancers	HUES48 Cell Line	embryonic stem cell

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