Variant report

Variant	rs2471106
Chromosome Location	chr5:79254118-79254119
allele	A/G
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:19)

rs_ID	r²[population]
rs10041404	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10064975	0.93[JPT][hapmap]
rs10065778	0.94[EUR][1000 genomes]
rs1032341	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1032342	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs2451929	0.80[EUR][1000 genomes]
rs2451930	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2471105	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2471107	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2471108	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2471109	0.80[EUR][1000 genomes]
rs6453494	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6860568	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6865678	0.81[EUR][1000 genomes]
rs923634	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs923636	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9293795	0.80[EUR][1000 genomes]
rs963423	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs963424	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021113	chr5:79034662-79289828	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv1822393	chr5:79195538-79260489	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	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
rs2471106	MTX3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79251800-79257600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:79252400-79257400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:79252600-79256800	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:79252600-79257800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:79252600-79258200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:79252800-79258000	Weak transcription	NH-A	brain
7	chr5:79252800-79258200	Weak transcription	HSMM	muscle
8	chr5:79253400-79257400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:79253600-79257600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr5:79253600-79257600	Weak transcription	NHEK	skin
11	chr5:79253600-79257800	Weak transcription	HMEC	breast
12	chr5:79254000-79257400	Weak transcription	Foreskin Keratinocyte 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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