Variant report

Variant	rs2601494
Chromosome Location	chr2:208991487-208991488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1020581	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10497893	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11677829	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13034094	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1470826	0.92[JPT][hapmap]
rs2289917	0.83[CEU][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs2601492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2601493	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2601495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2854722	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34126491	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34252721	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34577840	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34765959	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35960349	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55770589	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55999272	0.82[EUR][1000 genomes]
rs6709879	0.81[AMR][1000 genomes]
rs6751131	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv875744	chr2:208952810-208994045	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv875745	chr2:208969865-208994045	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv875747	chr2:208990345-209042963	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2601494	SNORD114-6	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208984600-208994200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:208989400-208999800	Weak transcription	Pancreas	Pancrea
3	chr2:208990400-208994400	Weak transcription	HepG2	liver
4	chr2:208990400-208995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:208990800-208994000	Weak transcription	Fetal Intestine Large	intestine
6	chr2:208990800-208994200	Weak transcription	Fetal Intestine Small	intestine

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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