Variant report

Variant	rs17152020
Chromosome Location	chr7:50549859-50549860
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1037351	0.84[AFR][1000 genomes]
rs1137337	0.93[AFR][1000 genomes]
rs11575387	0.86[LWK][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs11575422	0.82[AFR][1000 genomes]
rs11575438	0.95[AFR][1000 genomes]
rs11575453	0.92[JPT][hapmap]
rs17133853	0.83[LWK][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs2167364	0.84[ASW][hapmap];0.81[LWK][hapmap];0.86[MKK][hapmap];0.84[AFR][1000 genomes]
rs2329368	0.92[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes]
rs3779084	0.91[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4490786	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]
rs56069386	0.95[AFR][1000 genomes]
rs58085392	0.94[AFR][1000 genomes]
rs59239231	0.95[AFR][1000 genomes]
rs6592961	0.81[CEU][hapmap];0.91[GIH][hapmap];0.80[EUR][1000 genomes]
rs6951648	0.83[LWK][hapmap];0.95[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs7808025	0.81[CEU][hapmap]
rs880028	1.00[CEU][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[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
rs17152020	C7orf72	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50535800-50553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:50543600-50595000	Weak transcription	Liver	Liver
3	chr7:50545800-50565800	Weak transcription	HepG2	liver
4	chr7:50548800-50556600	Weak transcription	Fetal Intestine Small	intestine
5	chr7:50548800-50559600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr7:50548800-50559800	Weak transcription	Fetal Intestine Large	intestine
7	chr7:50548800-50564400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:50549600-50550400	Enhancers	Stomach Mucosa	stomach

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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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