Variant report

Variant	rs10876866
Chromosome Location	chr12:56445366-56445367
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000258345	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000257553	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000135482	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1131017	0.84[ASN][1000 genomes]
rs1689510	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1701704	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1702877	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2017445	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2456973	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2640562	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2640564	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34415530	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741499	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4759229	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61938962	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61938963	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs705696	0.80[AMR][1000 genomes]
rs705704	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs705705	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7302200	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs772921	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10876866	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL
rs10876866	RAB5B	cis	Muscle Skeletal	GTEx
rs10876866	AC034102.1	cis	Muscle Skeletal	GTEx
rs10876866	SUOX	cis	Thyroid	GTEx
rs10876866	DEFB124	trans	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56437000-56447200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:56437000-56472800	Weak transcription	Right Atrium	heart
3	chr12:56437800-56450000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:56439600-56447200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:56439600-56448800	Weak transcription	HSMMtube	muscle
6	chr12:56439600-56449600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:56439800-56448600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:56440000-56445400	Weak transcription	Placenta	Placenta
9	chr12:56440000-56448600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:56440200-56446000	Weak transcription	HSMM	muscle
11	chr12:56440400-56445600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:56440400-56448600	Weak transcription	HMEC	breast
13	chr12:56440600-56448400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:56440600-56448600	Weak transcription	A549	lung
15	chr12:56440800-56454000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:56440800-56455600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:56441000-56446400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr12:56441000-56448400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:56441200-56448600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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