Variant report

Variant	rs12908295
Chromosome Location	chr15:49789245-49789246
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11070712	1.00[AFR][1000 genomes]
rs12324090	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592839	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594926	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12900911	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12901023	1.00[AFR][1000 genomes]
rs12901631	1.00[AFR][1000 genomes]
rs12906292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12907986	1.00[AFR][1000 genomes]
rs12909835	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12913210	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12913379	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12913571	0.93[ASN][1000 genomes]
rs12913643	1.00[AFR][1000 genomes]
rs12913706	1.00[AFR][1000 genomes]
rs1429555	1.00[ASW][hapmap]
rs16962583	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs16962673	1.00[ASW][hapmap];1.00[AFR][1000 genomes]
rs2007443	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34134305	1.00[AFR][1000 genomes]
rs34212162	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34291739	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34377746	1.00[AFR][1000 genomes]
rs34461215	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34492504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34531968	1.00[AFR][1000 genomes]
rs34605270	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34737835	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34918968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34951376	1.00[AFR][1000 genomes]
rs34982209	1.00[AFR][1000 genomes]
rs35091054	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35112372	1.00[AFR][1000 genomes]
rs35145376	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35224895	1.00[AFR][1000 genomes]
rs35240887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35543719	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35563735	1.00[AFR][1000 genomes]
rs35683135	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35686890	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35699093	1.00[AFR][1000 genomes]
rs35799750	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36048625	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36106985	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36114417	1.00[AFR][1000 genomes]
rs4304966	1.00[AFR][1000 genomes]
rs4407014	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55662230	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55691379	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56053668	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56248339	1.00[AFR][1000 genomes]
rs66535408	1.00[AFR][1000 genomes]
rs67031905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71467682	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71467683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71467692	1.00[AFR][1000 genomes]
rs7175275	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72729117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72729172	1.00[AFR][1000 genomes]
rs8025420	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8029303	0.93[ASN][1000 genomes]
rs8030269	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9972602	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9263	chr15:49734435-49809465	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1043119	chr15:49760222-49844366	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1039185	chr15:49786255-49844366	Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12908295	FRMD5	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49781800-49789800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:49783600-49789800	Enhancers	Hela-S3	cervix
3	chr15:49787000-49789600	Enhancers	Osteobl	bone
4	chr15:49787600-49794800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:49788200-49789400	Weak transcription	Ovary	ovary
6	chr15:49788400-49789400	Enhancers	Muscle Satellite Cultured Cells	--
7	chr15:49788400-49789600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:49788800-49790200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:49789000-49789800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:49789000-49789800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:49789000-49789800	Enhancers	Rectal Smooth Muscle	rectum
12	chr15:49789000-49790400	Enhancers	Colon Smooth Muscle	Colon
13	chr15:49789200-49789800	Enhancers	NHLF	lung

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