Variant report

Variant	rs7560562
Chromosome Location	chr2:234912215-234912216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2052029	0.87[YRI][hapmap]
rs2052030	0.82[YRI][hapmap]
rs2190951	0.80[CHD][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap]
rs4664000	0.92[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4664001	0.80[CHD][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap]
rs6431650	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6431651	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6431652	0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6721761	0.91[GIH][hapmap];0.89[TSI][hapmap]
rs6727222	0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6734618	1.00[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.80[JPT][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7560562	PDE6D	cis	parietal	SCAN
rs7560562	UGT1A1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234898600-234912400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:234903000-234912400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:234908400-234912600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:234909600-234912600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:234909600-234919000	Strong transcription	Liver	Liver
6	chr2:234911200-234912400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:234912000-234912600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:234912000-234912600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:234912000-234912600	Enhancers	A549	lung
10	chr2:234912000-234914000	Enhancers	NHDF-Ad	bronchial
11	chr2:234912200-234912400	Flanking Active TSS	Osteobl	bone
12	chr2:234912200-234912800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:234912200-234913600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:234912200-234913600	Enhancers	NH-A	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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