Variant report

Variant	rs12668645
Chromosome Location	chr7:39762480-39762481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39665096..39667977-chr7:39762089..39764682,3	K562	blood:
2	chr7:39630501..39633434-chr7:39759020..39762831,5	K562	blood:
3	chr7:39760057..39765659-chr7:39765782..39774778,12	K562	blood:
4	chr7:39761757..39763732-chr7:39771479..39773340,2	MCF-7	breast:
5	chr7:39747835..39755058-chr7:39757872..39764388,13	K562	blood:
6	chr7:39678848..39680622-chr7:39760404..39763010,2	K562	blood:
7	chr7:39660254..39665233-chr7:39756811..39764394,13	K562	blood:
8	chr7:39759344..39763475-chr7:39764953..39775706,19	K562	blood:
9	chr7:39604771..39607441-chr7:39760385..39762790,2	K562	blood:
10	chr7:39745397..39755065-chr7:39757582..39762895,14	K562	blood:
11	chr7:39761591..39763196-chr7:39784084..39786176,2	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction
ENSG00000188185	Chromatin interaction
ENSG00000241127	Chromatin interaction
ENSG00000227172	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10231409	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10486802	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11770964	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12666517	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17508585	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107707	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34821005	0.86[EUR][1000 genomes]
rs62454689	0.88[EUR][1000 genomes]
rs6462943	0.87[EUR][1000 genomes]
rs7796021	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7799721	0.85[EUR][1000 genomes];0.97[ASN][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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12668645	LINC00265	cis	Thyroid	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39760800-39762800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr7:39761000-39762600	Active TSS	K562	blood
3	chr7:39761000-39762800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:39761200-39762800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:39761200-39764400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:39761800-39763000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr7:39762200-39762800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr7:39762200-39766400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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