Variant report

Variant	rs11779177
Chromosome Location	chr8:125937760-125937761
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:125566501..125569219-chr8:125936752..125938690,2	MCF-7	breast:
2	chr8:125826307..125827972-chr8:125936472..125938461,2	MCF-7	breast:
3	chr8:125935909..125938271-chr8:125963994..125966987,3	MCF-7	breast:
4	chr8:125604579..125606037-chr8:125936216..125937900,23	MCF-7	breast:
5	chr8:125927702..125929777-chr8:125936123..125937814,2	MCF-7	breast:
6	chr8:125549812..125552337-chr8:125936366..125938525,2	MCF-7	breast:
7	chr8:125865723..125867850-chr8:125937365..125941183,3	MCF-7	breast:
8	chr8:125933161..125934935-chr8:125937599..125940481,2	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000170873	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000255491	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11786449	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs13273002	0.81[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1427088	0.85[YRI][hapmap]
rs16900090	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16900098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1820535	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4409410	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5012401	0.89[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs60275472	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891434	chr8:125630655-126324432	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1030803	chr8:125868684-125969635	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1024405	chr8:125868684-125971035	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1020502	chr8:125868684-125972572	Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11779177	NSMCE2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125936400-125937800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr8:125936600-125941200	Weak transcription	K562	blood
3	chr8:125937000-125938400	Enhancers	Left Ventricle	heart
4	chr8:125937200-125938200	Enhancers	Lung	lung
5	chr8:125937400-125938200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr8:125937400-125938600	Weak transcription	HMEC	breast
7	chr8:125937400-125939200	Weak transcription	Esophagus	oesophagus
8	chr8:125937600-125951600	Weak transcription	Right Atrium	heart

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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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