Variant report

Variant	rs338625
Chromosome Location	chr5:113762810-113762811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1013168	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1072922	0.88[JPT][hapmap]
rs12188044	0.86[JPT][hapmap]
rs13155731	0.88[JPT][hapmap]
rs13163662	0.88[JPT][hapmap]
rs13173796	0.88[JPT][hapmap]
rs13174521	0.88[JPT][hapmap]
rs13176052	0.88[JPT][hapmap]
rs13179135	0.86[JPT][hapmap]
rs13181189	0.86[JPT][hapmap]
rs13183393	0.88[JPT][hapmap]
rs13184658	0.88[JPT][hapmap]
rs13186627	0.88[JPT][hapmap]
rs13187753	0.88[JPT][hapmap]
rs13190428	0.88[JPT][hapmap]
rs1457760	0.88[JPT][hapmap]
rs1457762	0.88[JPT][hapmap]
rs163210	0.83[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs163211	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168090	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2125146	0.88[JPT][hapmap]
rs2900084	0.84[ASN][1000 genomes]
rs337683	0.87[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs337684	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs337685	0.81[CEU][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs337689	0.93[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs337691	0.81[CEU][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs337695	0.83[CEU][hapmap];0.81[ASN][1000 genomes]
rs337699	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs337704	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs337705	0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs337707	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs337708	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs337709	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337710	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs337711	0.88[JPT][hapmap];0.86[EUR][1000 genomes]
rs337712	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs337714	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338622	0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338623	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs338663	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338664	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs338666	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36938	0.85[CHB][hapmap]
rs36946	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs36947	0.88[ASN][1000 genomes]
rs36949	0.88[JPT][hapmap]
rs36950	0.88[JPT][hapmap]
rs3857431	0.88[JPT][hapmap]
rs388084	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs4705504	0.88[JPT][hapmap]
rs4705665	0.88[JPT][hapmap]
rs4705667	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4705668	0.88[JPT][hapmap]
rs6859284	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs921981	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830451	chr5:113684301-113829833	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv882729	chr5:113743628-114497708	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs338625	COMMD10	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:113756400-113770000	Weak transcription	Fetal Heart	heart
2	chr5:113756600-113770200	Weak transcription	Liver	Liver
3	chr5:113760000-113770000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:113760200-113771600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:113761600-113769800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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