Variant report

Variant	rs12909153
Chromosome Location	chr15:56374765-56374766
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10152826	0.88[CEU][hapmap]
rs10162834	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10163161	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11632218	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11858173	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11858245	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12899534	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13379820	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17238601	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1829543	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2414466	0.82[CEU][hapmap]
rs2460649	0.96[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap]
rs2465405	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap]
rs2584689	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2682030	0.80[EUR][1000 genomes]
rs2682031	1.00[CEU][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs2682032	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2713922	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs2713934	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2713937	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2713939	0.80[EUR][1000 genomes]
rs2718924	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs2947023	0.80[EUR][1000 genomes]
rs35840822	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56274791	0.84[EUR][1000 genomes]
rs60138831	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62044114	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6493836	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7170102	0.92[EUR][1000 genomes]
rs748344	0.92[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8041422	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs894415	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.81[EUR][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	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12909153	RFXDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56363600-56383800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr15:56369800-56385600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:56374000-56375400	Enhancers	Placenta	Placenta
4	chr15:56374200-56375000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:56374200-56375000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr15:56374200-56375000	Enhancers	HMEC	breast
7	chr15:56374200-56375000	Enhancers	NHEK	skin
8	chr15:56374400-56374800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:56374600-56374800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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