Variant report

Variant	rs12130014
Chromosome Location	chr1:85297814-85297815
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12047733	0.89[ASN][1000 genomes]
rs1326002	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1409213	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1409214	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4907007	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9726410	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9729034	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[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	nsv830448	chr1:85294094-85491110	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12130014	CLCA3P	cis	parietal	SCAN
rs12130014	WDR63	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85289400-85330800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:85291000-85300000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:85291200-85301000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:85294400-85299400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:85294600-85299200	Weak transcription	HMEC	breast
6	chr1:85294600-85300400	Weak transcription	Fetal Heart	heart
7	chr1:85296000-85300200	Weak transcription	NHLF	lung
8	chr1:85296400-85299200	Weak transcription	Pancreas	Pancrea
9	chr1:85296600-85299200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:85296600-85312800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:85296800-85299000	Weak transcription	NHEK	skin
12	chr1:85297000-85299400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:85297800-85298000	Enhancers	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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