Variant report

Variant	rs6540754
Chromosome Location	chr1:212878652-212878653
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10779582	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11120005	0.84[ASN][1000 genomes]
rs12239017	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1580991	0.84[ASN][1000 genomes]
rs1580992	0.84[ASN][1000 genomes]
rs1605420	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4548508	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4951458	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6665489	0.84[ASN][1000 genomes]
rs6670373	0.84[ASN][1000 genomes]
rs6678961	0.84[ASN][1000 genomes]
rs6688947	0.85[ASN][1000 genomes]
rs6703982	0.84[ASN][1000 genomes]
rs9651103	0.82[ASN][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	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6540754	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs6540754	SNFT	Cis_1M	lymphoblastoid	RTeQTL
rs6540754	FLVCR1-AS1	cis	Whole Blood	GTEx
rs6540754	FLVCR1-AS1	cis	lung	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212877800-212879600	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr1:212878200-212879400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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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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