Variant report

Variant	rs2608938
Chromosome Location	chr6:131826720-131826721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12195206	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13193371	0.89[ASN][1000 genomes]
rs1572212	0.88[ASN][1000 genomes]
rs2246014	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2446222	0.83[ASN][1000 genomes]
rs2608899	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2608902	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2608930	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2781635	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2781641	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2807278	0.83[ASN][1000 genomes]
rs3895535	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv515476	chr6:131615425-132228577	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv1839224	chr6:131703293-131834119	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2829868	chr6:131729859-131898208	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv886667	chr6:131807510-131876943	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv886668	chr6:131814865-131954797	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2608938	ARG1	cis	Whole Blood	GTEx
rs2608938	ARG1	cis	lung	GTEx
rs2608938	ARG1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131819800-131830800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:131824800-131828600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:131824800-131830000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:131825400-131830600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:131825400-131830800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:131826200-131826800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:131826600-131830600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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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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