Variant report

Variant	rs865720
Chromosome Location	chr12:86490906-86490907
allele	A/C
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:37)

rs_ID	r²[population]
rs10779231	0.86[CEU][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs10863135	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs10863146	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs10863149	0.80[CEU][hapmap]
rs10863150	0.80[ASN][1000 genomes]
rs10863162	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863163	0.90[YRI][hapmap]
rs11117146	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs11117167	0.80[ASN][1000 genomes]
rs11513957	0.83[CEU][hapmap];0.91[JPT][hapmap]
rs12298174	0.82[YRI][hapmap]
rs12301701	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12308575	0.96[YRI][hapmap]
rs12318815	0.82[JPT][hapmap]
rs12809288	0.82[ASN][1000 genomes]
rs1354258	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1393612	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502799	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1502800	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6539935	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs6539941	0.84[ASN][1000 genomes]
rs6539942	0.91[CEU][hapmap];0.84[ASN][1000 genomes]
rs7136697	0.86[YRI][hapmap]
rs7300073	0.91[JPT][hapmap]
rs7301280	0.84[CEU][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7305869	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7313373	0.83[CEU][hapmap];0.91[JPT][hapmap]
rs7313442	0.83[CEU][hapmap];0.91[JPT][hapmap]
rs7314272	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs7397730	0.92[JPT][hapmap]
rs7485285	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs7955173	0.90[JPT][hapmap]
rs7966352	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7975457	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7978562	0.83[CEU][hapmap];0.92[JPT][hapmap]
rs8181635	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs952851	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

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
rs865720	MGAT4C	cis	Nerve Tibial	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86489800-86491400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:86490400-86491000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr12:86490400-86491400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr12:86490400-86491600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr12:86490600-86491200	Enhancers	Fetal Lung	lung

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