Variant report

Variant	rs7278258
Chromosome Location	chr21:47256810-47256811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11700891	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11908836	0.88[CHB][hapmap]
rs11911348	0.82[CHB][hapmap]
rs2277814	0.82[CHB][hapmap]
rs2330328	0.91[CHB][hapmap]
rs2838977	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs2839023	0.91[CHB][hapmap]
rs2839024	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs2839025	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs2839078	0.83[CHB][hapmap]
rs28478132	0.81[ASN][1000 genomes]
rs4818799	0.81[AMR][1000 genomes]
rs4819138	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs4819142	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs725930	0.82[CHB][hapmap]
rs7280089	0.82[CHB][hapmap]
rs741954	0.83[CHB][hapmap]
rs743351	0.81[ASN][1000 genomes]
rs8133338	0.82[CHB][hapmap]
rs909429	0.82[ASN][1000 genomes]
rs9977276	0.82[CHB][hapmap]
rs9977594	0.82[CHB][hapmap]
rs9984438	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
10	nsv914078	chr21:47218744-47311686	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
11	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
12	esv2756755	chr21:47243032-47319768	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	esv2758821	chr21:47243032-47319768	Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
14	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7278258	PCBP3	cis	Artery Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47217800-47260400	Weak transcription	Right Atrium	heart
2	chr21:47241600-47257400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr21:47241800-47257600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:47247000-47257600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr21:47247200-47257000	Weak transcription	Spleen	Spleen
6	chr21:47248000-47257200	Weak transcription	Primary T cells from cord blood	blood
7	chr21:47251000-47258800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr21:47253200-47258000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr21:47253200-47258600	Weak transcription	NHEK	skin
10	chr21:47253400-47257800	Strong transcription	Thymus	Thymus
11	chr21:47253400-47259000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr21:47253800-47258200	Weak transcription	HSMM	muscle
13	chr21:47254000-47258200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr21:47254200-47259200	Weak transcription	HMEC	breast
15	chr21:47254600-47257600	Weak transcription	Brain Anterior Caudate	brain
16	chr21:47255200-47257200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr21:47255200-47259800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr21:47255400-47257200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:47255600-47257200	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr21:47255600-47257800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr21:47255600-47257800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr21:47255800-47257000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr21:47256000-47257400	Enhancers	Fetal Lung	lung
24	chr21:47256200-47257200	Enhancers	Fetal Kidney	kidney
25	chr21:47256200-47258200	Enhancers	NHDF-Ad	bronchial
26	chr21:47256400-47259200	Weak transcription	HSMMtube	muscle
27	chr21:47256600-47257000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr21:47256600-47257200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr21:47256600-47257600	Enhancers	Dnd41	blood
30	chr21:47256600-47259200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr21:47256600-47260600	Weak transcription	Fetal Brain Male	brain
32	chr21:47256800-47257200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr21:47256800-47257200	Weak transcription	Brain Substantia Nigra	brain
34	chr21:47256800-47257200	Enhancers	Fetal Thymus	thymus
35	chr21:47256800-47258000	Enhancers	Brain Hippocampus Middle	brain

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