Variant report

Variant	rs6680707
Chromosome Location	chr1:247376950-247376951
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11811599	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12083552	0.89[AFR][1000 genomes]
rs1343544	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4314914	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55768801	0.89[EUR][1000 genomes]
rs56338561	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57861883	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60050650	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61636449	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691539	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6693807	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6699577	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6704060	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
3	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
6	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
8	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
9	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6680707	MIR3916	cis	Whole Blood	GTEx
rs6680707	RP11-488L18.10	cis	Artery Tibial	GTEx
rs6680707	RP11-488L18.10	cis	lung	GTEx
rs6680707	LOC729806	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247374200-247379600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:247374600-247377200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:247374600-247377200	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr1:247374600-247377200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:247374600-247379600	Weak transcription	Fetal Thymus	thymus
6	chr1:247374800-247377000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr1:247375000-247377200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:247375600-247377200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr1:247376200-247377200	Enhancers	GM12878-XiMat	blood
10	chr1:247376600-247379800	Weak transcription	K562	blood
11	chr1:247376800-247377000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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