Variant report

Variant	rs1554824
Chromosome Location	chr2:177646988-177646989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10930752	0.84[ASN][1000 genomes]
rs12467333	0.82[ASN][1000 genomes]
rs12469087	0.86[JPT][hapmap]
rs12470292	0.83[CHD][hapmap]
rs12477377	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12611718	0.80[ASN][1000 genomes]
rs12618099	0.80[ASN][1000 genomes]
rs12693106	0.83[CHD][hapmap]
rs1437724	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1554012	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17670224	0.86[AMR][1000 genomes]
rs4021394	0.86[JPT][hapmap]
rs4600700	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs62174238	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706043	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6758766	0.82[ASN][1000 genomes]
rs7569150	0.81[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][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	nsv527737	chr2:177538266-177692572	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv583686	chr2:177538266-177692572	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006500	chr2:177548521-177707097	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1554824	CST3	trans	lymphoblastoid	seeQTL
rs1554824	OLA1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177628800-177655400	Weak transcription	Ovary	ovary
2	chr2:177644000-177649600	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:177644200-177649000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:177645800-177647000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
5	chr2:177646200-177647200	ZNF genes & repeats	Dnd41	blood
6	chr2:177646400-177647000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr2:177646600-177648200	Weak transcription	Spleen	Spleen

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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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