Variant report

Variant	rs1507334
Chromosome Location	chr1:209411971-209411972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10779504	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863764	0.95[AFR][1000 genomes]
rs10863765	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11119245	0.83[AFR][1000 genomes]
rs1354849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1933601	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2135817	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2660644	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2788152	0.81[JPT][hapmap]
rs4844466	0.95[AFR][1000 genomes]
rs6419460	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6674807	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6690080	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693967	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7550487	0.86[AFR][1000 genomes]
rs9943143	0.86[CEU][hapmap]

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	nsv832481	chr1:209371276-209540333	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832492	chr1:209383771-209589312	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv1008555	chr1:209409577-209416496	Strong transcription Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1507334	ETNK2	cis	cerebellum	SCAN
rs1507334	YOD1	cis	parietal	SCAN
rs1507334	CAMK1G	cis	cerebellum	SCAN
rs1507334	PPP1R15B	cis	cerebellum	SCAN
rs1507334	SNRPE	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209409800-209422200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209411600-209412000	Enhancers	HMEC	breast
3	chr1:209411600-209412200	Enhancers	NHEK	skin
4	chr1:209411600-209412400	Enhancers	HUVEC	blood vessel
5	chr1:209411800-209412200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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