Variant report

Variant	rs2183628
Chromosome Location	chr14:56390908-56390909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1107097	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12434440	0.82[CHD][hapmap]
rs17090687	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17090690	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1952882	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2150509	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2342851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4898878	0.90[ASN][1000 genomes]
rs7144669	0.94[CEU][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7146394	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7146594	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7149543	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs874656	0.96[EUR][1000 genomes];1.00[ASN][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	nsv901966	chr14:56160904-56436203	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv901977	chr14:56213392-56492996	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv34106	chr14:56346245-56550642	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2183628	GMFB	cis	parietal	SCAN
rs2183628	C14orf37	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56373200-56392000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:56380800-56394400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:56387200-56395800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr14:56389200-56393800	Weak transcription	Gastric	stomach
5	chr14:56389600-56391400	Weak transcription	Stomach Mucosa	stomach
6	chr14:56389800-56392600	Weak transcription	Pancreas	Pancrea

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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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