Variant report

Variant	rs10878378
Chromosome Location	chr12:66499512-66499513
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11176060	0.89[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1168735	0.91[EUR][1000 genomes]
rs1168765	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168766	1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168770	0.93[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1177578	0.93[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1183892	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs1184556	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1184884	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1185888	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs12823890	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1370126	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1436849	0.82[EUR][1000 genomes]
rs2576187	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2870782	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870783	0.82[ASN][1000 genomes]
rs4296075	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4328252	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975029	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7979576	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8793	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899213	chr12:66389968-66500036	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv832446	chr12:66393863-66501484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10878378	RP11-745O10.2	cis	Skin Sun Exposed Lower leg	GTEx
rs10878378	TMBIM4	cis	lesional skin	skin_eQTL
rs10878378	RP11-745O10.2	cis	Artery Tibial	GTEx
rs10878378	RP11-745O10.2	cis	Whole Blood	GTEx
rs10878378	RP11-745O10.2	cis	Artery Aorta	GTEx
rs10878378	RP11-745O10.2	cis	lung	GTEx
rs10878378	TMBIM4	Cis_1M	lymphoblastoid	RTeQTL
rs10878378	TMBIM4	cis	normal skin	skin_eQTL
rs10878378	RP11-745O10.2	cis	Thyroid	GTEx
rs10878378	RP11-745O10.2	cis	Esophagus Muscularis	GTEx
rs10878378	RP11-745O10.2	cis	Esophagus Mucosa	GTEx
rs10878378	RP11-745O10.2	cis	Heart Left Ventricle	GTEx
rs10878378	RP11-745O10.2	cis	Stomach	GTEx
rs10878378	TMBIM4	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66497200-66500800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:66497600-66500800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:66497800-66500800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:66498600-66500800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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