Variant report

Variant	rs2054617
Chromosome Location	chr2:213355890-213355891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10201067	0.88[CHB][hapmap]
rs10206719	0.81[CHD][hapmap]
rs1026882	0.88[CEU][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1283310	0.85[ASW][hapmap];0.88[CHB][hapmap]
rs13419353	0.88[CHB][hapmap]
rs1384293	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs1384294	0.80[EUR][1000 genomes]
rs1384295	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs1905139	0.88[CEU][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs2888093	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4106226	0.88[CHB][hapmap]
rs6435701	1.00[CHB][hapmap]
rs6435707	0.96[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7556832	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs7565622	0.88[CEU][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs972491	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs974968	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs979124	0.80[EUR][1000 genomes]

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	nsv1004573	chr2:213186537-213365252	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	nsv432024	chr2:213314899-213446726	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv948878	chr2:213345197-213534298	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	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
rs2054617	LANCL1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:213353400-213356200	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:213353400-213362200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:213353800-213356600	Weak transcription	Brain Angular Gyrus	brain
4	chr2:213354000-213356200	Weak transcription	Brain Substantia Nigra	brain
5	chr2:213354200-213359800	Weak transcription	Fetal Kidney	kidney
6	chr2:213355400-213356200	Enhancers	Fetal Heart	heart
7	chr2:213355800-213356600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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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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