Variant report

Variant	rs1647396
Chromosome Location	chr11:57401183-57401184
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1557522	0.92[AFR][1000 genomes]
rs1783826	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2081362	0.92[ASN][1000 genomes]
rs2511993	0.92[ASN][1000 genomes]
rs2511994	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2511996	0.90[ASN][1000 genomes]
rs2926664	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35196561	0.82[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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1647396	TIMM10	cis	Esophagus Muscularis	GTEx
rs1647396	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs1647396	TIMM10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57384400-57404800	Weak transcription	Fetal Lung	lung
2	chr11:57387600-57405200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:57389200-57404400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:57398400-57401200	Weak transcription	Placenta	Placenta
5	chr11:57398600-57405200	Weak transcription	Liver	Liver
6	chr11:57400200-57403200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:57400600-57401200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:57400600-57403800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr11:57401000-57402800	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr11:57401000-57403000	Enhancers	HMEC	breast
11	chr11:57401000-57403000	Enhancers	NHEK	skin
12	chr11:57401000-57405000	Weak transcription	Right Atrium	heart

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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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