Variant report

Variant	rs17710880
Chromosome Location	chr7:47876787-47876788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11765736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769398	0.86[JPT][hapmap]
rs12668946	0.89[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12673502	1.00[CEU][hapmap];0.84[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17545564	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs17627961	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17659868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17659956	0.92[CHD][hapmap]
rs17710874	1.00[CHB][hapmap];0.86[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123609	0.89[CEU][hapmap];0.84[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290386	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2348462	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs4724648	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4724650	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6951478	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6959021	0.89[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73692834	0.87[ASN][1000 genomes]
rs9639988	0.88[CEU][hapmap];0.83[CHB][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' 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
rs17710880	URGCP	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47852800-47879000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:47855000-47880200	Weak transcription	Lung	lung
3	chr7:47855800-47902400	Weak transcription	Adipose Nuclei	Adipose
4	chr7:47867200-47886000	Weak transcription	Right Atrium	heart
5	chr7:47867800-47886000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr7:47868200-47876800	Weak transcription	Left Ventricle	heart
7	chr7:47868600-47879200	Weak transcription	Pancreas	Pancrea
8	chr7:47868800-47886000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr7:47869800-47885400	Weak transcription	HSMMtube	muscle
10	chr7:47870000-47880200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:47873200-47876800	Weak transcription	Right Ventricle	heart
12	chr7:47875600-47878200	Enhancers	Fetal Muscle Leg	muscle
13	chr7:47875800-47877400	Enhancers	Fetal Muscle Trunk	muscle
14	chr7:47876000-47878200	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr7:47876200-47878200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:47876400-47877200	Enhancers	Fetal Heart	heart
17	chr7:47876400-47877200	Bivalent Enhancer	Fetal Stomach	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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