Variant report

Variant	rs3860492
Chromosome Location	chr2:190481745-190481746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11675304	0.81[EUR][1000 genomes]
rs11678005	0.90[TSI][hapmap]
rs11684519	0.81[EUR][1000 genomes]
rs13025114	0.80[ASN][1000 genomes]
rs13415781	0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs1437887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2099608	0.81[ASN][1000 genomes]
rs28454062	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4372939	0.90[TSI][hapmap]
rs4667292	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59901914	0.86[ASN][1000 genomes]
rs6735087	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6735185	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7580851	0.87[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs7587662	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7604386	0.87[JPT][hapmap]

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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3860492	FSIP2	cis	cerebellum	SCAN
rs3860492	WDR75	cis	parietal	SCAN
rs3860492	LOC51240	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190478600-190483800	Weak transcription	HepG2	liver
2	chr2:190479000-190484000	Weak transcription	A549	lung
3	chr2:190479000-190503800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:190479200-190484200	Weak transcription	HUVEC	blood vessel
5	chr2:190479600-190482200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:190479600-190485200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:190479800-190483400	Weak transcription	Fetal Heart	heart
8	chr2:190480000-190483800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:190480600-190482200	Weak transcription	Placenta	Placenta

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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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