Variant report

Variant	rs10248125
Chromosome Location	chr7:78362917-78362918
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10243919	0.95[ASN][1000 genomes]
rs10248911	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10808167	0.81[CEU][hapmap]
rs10953684	0.96[ASN][1000 genomes]
rs1118936	0.81[CEU][hapmap]
rs1207870	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs1207871	0.83[CEU][hapmap]
rs1207872	0.83[CEU][hapmap]
rs1207875	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs1207881	0.80[CEU][hapmap]
rs1207882	0.80[CEU][hapmap]
rs1209401	0.83[CHB][hapmap]
rs1859327	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs323130	0.80[MKK][hapmap]
rs4730480	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6951046	0.80[CEU][hapmap];0.82[CHB][hapmap];0.80[MKK][hapmap]
rs6965150	0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7807809	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[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	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1019355	chr7:78319575-78399845	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv607657	chr7:78329795-78483211	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10248125	WBSCR16	cis	cerebellum	SCAN
rs10248125	SEMA3C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78355600-78363400	Weak transcription	Brain Anterior Caudate	brain
2	chr7:78361000-78363200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:78361600-78363800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:78361600-78372000	Weak transcription	Aorta	Aorta
5	chr7:78362400-78366200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:78362800-78372200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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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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