Variant report

Variant	rs932559
Chromosome Location	chr2:31552902-31552903
allele	A/C
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:8)

rs_ID	r²[population]
rs1042039	0.92[ASW][hapmap];0.89[CEU][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10490361	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1054889	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs12614330	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs169596	0.86[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs207429	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2268800	0.84[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs736492	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv949028	chr2:31502801-31665108	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv2762446	chr2:31521093-31610311	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs932559	SLC30A3	cis	cerebellum	SCAN
rs932559	UCN	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31528200-31554000	Weak transcription	Right Ventricle	heart
2	chr2:31547800-31556200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:31548000-31556000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:31548000-31556000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:31548000-31556200	Weak transcription	Liver	Liver
6	chr2:31548000-31556400	Weak transcription	HMEC	breast
7	chr2:31548000-31557600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:31548000-31558400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:31548000-31634600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:31548200-31553600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:31548400-31558600	Weak transcription	NHEK	skin
12	chr2:31550600-31553600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:31551800-31553000	Enhancers	Fetal Intestine Small	intestine
14	chr2:31552000-31553400	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:31552200-31554000	Weak transcription	Fetal Heart	heart
16	chr2:31552400-31553400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:31552400-31556000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:31552800-31557000	Weak transcription	Fetal Intestine Large	intestine

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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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