Variant report

Variant	rs858972
Chromosome Location	chr6:27154361-27154362
allele	A/G
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	chr6:27154198..27156038-chr6:27159087..27161685,2	MCF-7	breast:
2	chr6:27145218..27148337-chr6:27151646..27158450,9	MCF-7	breast:
3	chr6:27113069..27114668-chr6:27153428..27155363,2	K562	blood:
4	chr6:27150672..27153341-chr6:27153761..27155795,3	MCF-7	breast:
5	chr6:27153641..27158263-chr6:27858563..27861801,5	K562	blood:
6	chr6:27144640..27146653-chr6:27152847..27154919,2	K562	blood:
7	chr6:27114939..27117742-chr6:27153749..27157823,5	K562	blood:
8	chr6:27154260..27155926-chr6:27167713..27170180,2	K562	blood:
9	chr6:27148219..27154668-chr6:27154722..27158254,9	K562	blood:
10	chr6:27154220..27156812-chr6:27776425..27779440,4	K562	blood:
11	chr6:27143412..27146140-chr6:27152536..27156532,5	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000265565	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000203813	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1102558	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1102559	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1102560	0.83[EUR][1000 genomes]
rs1102564	0.84[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[EUR][1000 genomes]
rs2753120	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713069	0.85[JPT][hapmap]
rs60266855	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs858967	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858968	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858969	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858970	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858973	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs858976	0.88[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs858980	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs858972	BTN3A2	cis	cerebellum	SCAN
rs858972	ZNF391	cis	cerebellum	SCAN
rs858972	BTN3A3	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27146600-27155800	Weak transcription	Spleen	Spleen
2	chr6:27146800-27155400	Weak transcription	Adipose Nuclei	Adipose
3	chr6:27147000-27155000	Weak transcription	Right Atrium	heart
4	chr6:27147000-27155600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:27153400-27154400	Enhancers	K562	blood

Quick Search:

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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