Variant report

Variant	rs508742
Chromosome Location	chr1:172175115-172175116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10911299	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2586393	0.88[ASW][hapmap]
rs2586416	0.88[ASW][hapmap]
rs479960	0.81[MEX][hapmap]
rs484686	0.88[ASW][hapmap];0.88[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs492746	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532688	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs562932	0.80[ASN][1000 genomes]
rs583578	0.80[CEU][hapmap];0.81[MEX][hapmap]
rs589209	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598562	0.85[JPT][hapmap];0.85[MEX][hapmap]
rs633592	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6424865	0.88[ASW][hapmap]
rs655853	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6689455	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs672740	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs681398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs683128	0.81[GIH][hapmap]
rs687041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[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	nsv1000079	chr1:172146935-172230545	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv465650	chr1:172175115-172247127	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv548192	chr1:172175115-172247127	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs508742	C1orf112	cis	cerebellum	SCAN
rs508742	FMO1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172169200-172176000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:172172800-172175200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:172172800-172175600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:172173800-172176400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:172174400-172175400	Weak transcription	GM12878-XiMat	blood
6	chr1:172175000-172176000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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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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