Variant report

Variant	rs4954016
Chromosome Location	chr2:133749102-133749103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1370598	0.82[EUR][1000 genomes]
rs1437897	0.82[EUR][1000 genomes]
rs4954015	0.81[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4954017	0.94[ASN][1000 genomes]
rs4954018	0.95[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs4954019	0.82[EUR][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	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv875138	chr2:133410921-133761794	Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1004604	chr2:133658116-133761794	Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv916805	chr2:133664765-133924973	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv834381	chr2:133722671-133897994	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv834382	chr2:133728399-133891418	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv999703	chr2:133734955-133817962	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv535926	chr2:133734955-133817962	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4954016	CCDC115	cis	cerebellum	SCAN
rs4954016	IMP4	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133736400-133749200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:133739600-133753000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:133741200-133753400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:133741400-133749800	Weak transcription	Fetal Stomach	stomach
5	chr2:133743400-133750600	Weak transcription	NHLF	lung
6	chr2:133744200-133754000	Weak transcription	Hela-S3	cervix
7	chr2:133745800-133753200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:133747800-133750200	Weak transcription	Ovary	ovary
9	chr2:133747800-133750600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:133748600-133749200	Enhancers	Small Intestine	intestine
11	chr2:133748600-133749800	Enhancers	Fetal Intestine Small	intestine
12	chr2:133748600-133751200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:133748800-133749400	Active TSS	Duodenum Mucosa	Duodenum
14	chr2:133748800-133749800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:133748800-133749800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:133749000-133749400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:133749000-133749400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr2:133749000-133749800	Weak transcription	Brain Hippocampus Middle	brain

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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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