Variant report

Variant	rs11678201
Chromosome Location	chr2:86639100-86639101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1113169	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11687162	0.92[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs11903855	0.92[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12617075	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs12714182	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs13420491	1.00[ASN][1000 genomes]
rs2113607	0.96[CEU][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes]
rs2367238	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832278	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs4832282	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs4832283	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6547680	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6708398	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6713586	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6756146	0.96[CEU][hapmap]
rs7573005	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11678201	POLR1A	cis	cerebellum	SCAN
rs11678201	PTCD3	cis	cerebellum	SCAN
rs11678201	KDM3A	cis	cerebellum	SCAN
rs11678201	KDM3A	cis	parietal	SCAN
rs11678201	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs11678201	RNF103	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86638600-86639200	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr2:86638600-86640600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:86639000-86639200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr2:86639000-86640600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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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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