Variant report

Variant	rs12643456
Chromosome Location	chr4:76745593-76745594
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13101593	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13107337	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13124724	0.87[CHB][hapmap]
rs3796479	0.87[CHB][hapmap]
rs62321562	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6847598	1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3467669	chr4:76741328-76746326	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv3467670	chr4:76741328-76746326	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	esv3521067	chr4:76742178-76745626	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12643456	CDKL2	cis	parietal	SCAN
rs12643456	CDKL2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76736600-76763200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:76736800-76746400	Weak transcription	Brain Anterior Caudate	brain
3	chr4:76736800-76753000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:76737000-76753000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:76737600-76751000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:76738200-76748400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:76738200-76753000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:76738400-76751800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:76743800-76764800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:76744600-76745600	Enhancers	A549	lung
11	chr4:76744800-76745600	Enhancers	NH-A	brain
12	chr4:76745000-76745600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:76745000-76745600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:76745000-76745800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:76745000-76745800	Enhancers	Ovary	ovary

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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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