Variant report

Variant	rs16860127
Chromosome Location	chr3:112544367-112544368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112358959..112361432-chr3:112542934..112544575,2	MCF-7	breast:
2	chr3:112529420..112531231-chr3:112543770..112545710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1125377	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11918522	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1500877	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16860073	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs16860075	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs16860128	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16860141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1873041	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1948164	0.83[ASN][1000 genomes]
rs2037820	0.86[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs2078008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2087254	0.86[ASN][1000 genomes]
rs2129844	0.86[ASN][1000 genomes]
rs2173820	0.86[ASN][1000 genomes]
rs4292202	0.86[ASN][1000 genomes]
rs4390897	0.86[ASN][1000 genomes]
rs4682117	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4682119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66635385	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6770923	0.86[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs6773083	0.80[CEU][hapmap];0.90[MEX][hapmap]
rs6795521	0.84[CEU][hapmap]
rs6809029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6809039	1.00[JPT][hapmap]
rs72950332	0.86[ASN][1000 genomes]
rs72950361	0.86[ASN][1000 genomes]
rs7610094	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7610468	0.86[ASN][1000 genomes]
rs7625445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap]
rs7642393	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7642984	0.91[CHD][hapmap];0.82[TSI][hapmap]

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	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv877343	chr3:112470586-112597706	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16860127	C3orf17	cis	cerebellum	SCAN
rs16860127	ABHD10	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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