Variant report

Variant	rs346300
Chromosome Location	chr6:80574026-80574027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs103194	0.85[AMR][1000 genomes]
rs1555416	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs168304	0.83[AMR][1000 genomes]
rs182955	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs346278	0.83[AMR][1000 genomes]
rs346280	0.83[AMR][1000 genomes]
rs346287	0.82[AMR][1000 genomes]
rs346289	0.83[AMR][1000 genomes]
rs346293	0.85[AMR][1000 genomes]
rs346294	0.85[AMR][1000 genomes]
rs346295	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs346296	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs346298	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs346305	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4706805	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62411143	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][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	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1021143	chr6:80400195-80598163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	esv3693359	chr6:80539454-80606537	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs346300	hCT2332405	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80571000-80578200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:80573200-80574800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr6:80573200-80576800	Enhancers	Fetal Heart	heart
4	chr6:80573600-80574200	Enhancers	Brain Germinal Matrix	brain
5	chr6:80573600-80574400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:80573800-80574600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:80573800-80574600	Enhancers	Esophagus	oesophagus
8	chr6:80573800-80575400	Enhancers	Pancreas	Pancrea

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Input of quick search could be:

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

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