Variant report

Variant	rs2007540
Chromosome Location	chr15:78429340-78429341
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: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	chr15:78427835..78429477-chr15:78433034..78435107,2	MCF-7	breast:
2	chr15:78424791..78431116-chr15:78431151..78434947,7	MCF-7	breast:
3	chr15:78426143..78427664-chr15:78427813..78429713,2	K562	blood:
4	chr15:78425346..78429501-chr15:78464309..78466788,4	MCF-7	breast:
5	chr15:78426200..78429701-chr15:78439190..78443873,6	MCF-7	breast:
6	chr15:78422482..78425434-chr15:78426789..78430921,3	K562	blood:
7	chr15:78427990..78430130-chr15:78433537..78435555,2	K562	blood:
8	chr15:78427128..78429696-chr15:78439900..78441768,2	K562	blood:

No data

No data

No data

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11857947	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1542101	0.85[CHB][hapmap]
rs16969520	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs3784327	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3784331	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs6495274	0.80[ASN][1000 genomes]
rs72625800	0.87[AMR][1000 genomes]
rs8040395	0.80[ASN][1000 genomes]
rs9783722	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2007540	CYP11A1	cis	cerebellum	SCAN
rs2007540	IDH3A	cis	parietal	SCAN
rs2007540	SCAPER	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78424400-78433400	Weak transcription	Ovary	ovary
2	chr15:78424600-78440800	Weak transcription	HSMMtube	muscle
3	chr15:78424800-78431600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:78424800-78431800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:78425000-78440600	Weak transcription	Fetal Stomach	stomach
6	chr15:78425200-78431600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr15:78425400-78432000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:78425400-78432600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr15:78425400-78436800	Weak transcription	Adipose Nuclei	Adipose
10	chr15:78426000-78435800	Weak transcription	Thymus	Thymus
11	chr15:78426000-78440200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:78426400-78431600	Weak transcription	Small Intestine	intestine
13	chr15:78427200-78438600	Weak transcription	Placenta	Placenta
14	chr15:78427200-78439200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:78428200-78435400	Enhancers	Fetal Intestine Large	intestine
16	chr15:78428400-78431000	Enhancers	Duodenum Mucosa	Duodenum
17	chr15:78428600-78432200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:78428600-78435400	Enhancers	Fetal Intestine Small	intestine
19	chr15:78428800-78432200	Weak transcription	Stomach Mucosa	stomach

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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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