Variant report

Variant	rs1817686
Chromosome Location	chr7:137758670-137758671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10226024	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10265064	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10278929	0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10280600	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10954601	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11760991	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12111721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13243602	0.81[AMR][1000 genomes]
rs2352140	0.85[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28533201	0.81[AMR][1000 genomes]
rs28609414	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4728430	0.95[CHB][hapmap]
rs4732288	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57020142	0.83[AMR][1000 genomes]
rs6467734	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6943498	0.90[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8180809	0.84[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][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	nsv518070	chr7:137534627-137808839	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv831151	chr7:137711447-137865471	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	esv34048	chr7:137724092-138213119	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	nsv437032	chr7:137753091-137773291	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1817686	MKRN1	cis	cerebellum	SCAN
rs1817686	CALD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137754000-137758800	Weak transcription	Liver	Liver
2	chr7:137757600-137759600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
3	chr7:137757800-137761200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
4	chr7:137758000-137760200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:137758600-137759800	Enhancers	HMEC	breast
6	chr7:137758600-137761200	ZNF genes & repeats	HepG2	liver

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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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