Variant report

Variant	rs4490786
Chromosome Location	chr7:50544314-50544315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1037351	0.81[YRI][hapmap]
rs1137337	0.87[AFR][1000 genomes]
rs11575387	0.83[LWK][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs11575438	0.89[AFR][1000 genomes]
rs11575453	0.92[JPT][hapmap]
rs17133853	0.80[LWK][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap]
rs17152020	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2329368	0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3779084	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56069386	0.89[AFR][1000 genomes]
rs58085392	0.88[AFR][1000 genomes]
rs59239231	0.89[AFR][1000 genomes]
rs6592961	0.81[CEU][hapmap];0.91[GIH][hapmap]
rs6951648	0.80[LWK][hapmap];0.89[MKK][hapmap];0.90[YRI][hapmap]
rs7808025	0.81[CEU][hapmap]
rs880028	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.94[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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription 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
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv606905	chr7:50544063-50565963	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4490786	C7orf72	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50535800-50546800	Weak transcription	Pancreas	Pancrea
2	chr7:50535800-50553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:50536200-50545400	Weak transcription	Right Atrium	heart
4	chr7:50542000-50549600	Weak transcription	Stomach Mucosa	stomach
5	chr7:50542200-50545000	Weak transcription	HepG2	liver
6	chr7:50542200-50546000	Genic enhancers	Fetal Intestine Small	intestine
7	chr7:50543400-50546600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:50543600-50595000	Weak transcription	Liver	Liver
9	chr7:50544200-50544600	Strong transcription	Fetal Intestine Large	intestine
10	chr7:50544200-50548400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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