Variant report

Variant	rs419029
Chromosome Location	chr16:12054077-12054078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr16:12054020-12054170	Hela-S3	cervix:	n/a	n/a
2	ZNF384	chr16:12054011-12054435	K562	blood:	n/a	n/a
3	CTCF	chr16:12054077-12054370	K562	blood:	n/a	n/a

Variant related genes	Relation type
TNFRSF17	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs14817	1.00[AMR][1000 genomes]
rs153026	1.00[AMR][1000 genomes]
rs153027	1.00[AMR][1000 genomes]
rs1794329	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs251725	1.00[AMR][1000 genomes]
rs33628	1.00[AMR][1000 genomes]
rs33632	1.00[AMR][1000 genomes]
rs33634	1.00[AMR][1000 genomes]
rs33656	1.00[AMR][1000 genomes]
rs33658	1.00[AMR][1000 genomes]
rs370768	1.00[AMR][1000 genomes]
rs379936	1.00[AMR][1000 genomes]
rs386606	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs419040	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs426424	1.00[AMR][1000 genomes]
rs432140	1.00[AMR][1000 genomes]
rs434806	1.00[AMR][1000 genomes]
rs469657	1.00[AMR][1000 genomes]
rs636664	1.00[AMR][1000 genomes]
rs677507	1.00[AMR][1000 genomes]
rs73513691	1.00[AMR][1000 genomes]
rs73515603	1.00[AMR][1000 genomes]
rs73515605	1.00[AMR][1000 genomes]
rs73515607	1.00[AMR][1000 genomes]
rs73515608	1.00[AMR][1000 genomes]
rs73515629	1.00[AMR][1000 genomes]
rs73515632	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv571459	chr16:12046899-12062396	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv962195	chr16:12053526-12071576	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs419029	LTB	trans	lymphoblastoid	seeQTL
rs419029	RNASE6	trans	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12040400-12065400	Weak transcription	Fetal Intestine Small	intestine
2	chr16:12042200-12064400	Weak transcription	Fetal Stomach	stomach
3	chr16:12044800-12056400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr16:12048600-12064800	Weak transcription	Thymus	Thymus
5	chr16:12050400-12058200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr16:12052200-12067600	Weak transcription	Osteobl	bone
7	chr16:12052200-12069600	Weak transcription	Primary T cells from cord blood	blood
8	chr16:12052400-12055200	Enhancers	Primary B cells from peripheral blood	blood
9	chr16:12052400-12058600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr16:12052400-12066800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr16:12052600-12054400	Enhancers	Primary B cells from cord blood	blood
12	chr16:12053000-12058600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr16:12053000-12065800	Weak transcription	Placenta	Placenta
14	chr16:12053200-12058600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr16:12053400-12055400	Enhancers	GM12878-XiMat	blood
16	chr16:12053400-12057400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:12053400-12057400	Weak transcription	NHEK	skin
18	chr16:12053400-12058600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr16:12053400-12058800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr16:12053800-12057600	Weak transcription	Fetal Thymus	thymus
21	chr16:12054000-12056600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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