Variant report

Variant	rs425872
Chromosome Location	chr5:57919019-57919020
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs158978	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs292969	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs292990	0.92[GIH][hapmap]
rs386161	0.81[CEU][hapmap];0.92[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1029145	chr5:57905821-58141221	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830311	chr5:57912546-58105636	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs425872	IL31RA	cis	cerebellum	SCAN
rs425872	LRRC70	cis	cerebellum	SCAN
rs425872	CDC20B	cis	cerebellum	SCAN
rs425872	LRRC70	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57913400-57919200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:57917800-57919200	Enhancers	Stomach Mucosa	stomach
3	chr5:57918000-57919600	Enhancers	Left Ventricle	heart
4	chr5:57918000-57919800	Enhancers	Fetal Lung	lung
5	chr5:57918400-57924400	Weak transcription	Small Intestine	intestine
6	chr5:57918600-57919800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:57918800-57919800	Enhancers	Ovary	ovary
8	chr5:57918800-57920200	Enhancers	Fetal Stomach	stomach
9	chr5:57919000-57919200	Enhancers	Right Atrium	heart
10	chr5:57919000-57919400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr5:57919000-57919400	Active TSS	Fetal Brain Male	brain
12	chr5:57919000-57919600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:57919000-57919800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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