Variant report

Variant	rs4849360
Chromosome Location	chr2:111815871-111815872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10187034	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11123325	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13000374	0.82[CHD][hapmap];0.84[JPT][hapmap]
rs1384795	1.00[ASW][hapmap]
rs1483533	1.00[ASW][hapmap]
rs1483535	1.00[ASW][hapmap]
rs1821969	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1898846	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2128813	1.00[ASW][hapmap]
rs2880119	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4465771	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4848374	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6542248	1.00[ASW][hapmap]
rs6733493	1.00[ASW][hapmap]
rs6759108	0.86[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4849360	JHDM1D	trans	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111787800-111825400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:111810200-111816800	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:111811800-111816600	Enhancers	Primary B cells from cord blood	blood
4	chr2:111813600-111817600	Weak transcription	Lung	lung
5	chr2:111814600-111816000	Enhancers	Fetal Muscle Leg	muscle
6	chr2:111814800-111816000	Enhancers	Fetal Thymus	thymus
7	chr2:111815200-111817600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:111815600-111816600	Enhancers	GM12878-XiMat	blood

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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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