Variant report

Variant	rs6493836
Chromosome Location	chr15:56376535-56376536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10162834	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10163161	0.80[EUR][1000 genomes]
rs11632218	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11858173	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11858245	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12899534	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12909153	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13379820	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17238601	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1829543	0.89[ASN][1000 genomes]
rs2247838	0.88[ASN][1000 genomes]
rs2414466	0.83[ASN][1000 genomes]
rs2460649	0.87[ASN][1000 genomes]
rs2465969	0.87[ASN][1000 genomes]
rs2584689	0.89[ASN][1000 genomes]
rs2682030	0.89[ASN][1000 genomes]
rs2682031	0.89[ASN][1000 genomes]
rs2713922	0.87[ASN][1000 genomes]
rs2713937	0.89[ASN][1000 genomes]
rs2713939	0.89[ASN][1000 genomes]
rs2718924	0.87[ASN][1000 genomes]
rs35840822	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56274791	0.80[EUR][1000 genomes]
rs60138831	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62044114	0.81[EUR][1000 genomes]
rs7170102	0.88[EUR][1000 genomes]
rs748344	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs894415	0.88[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	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
rs6493836	RFXDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 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	chr15:56374800-56381600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:56375000-56381600	Weak transcription	HMEC	breast
5	chr15:56375000-56385000	Weak transcription	NHEK	skin
6	chr15:56375000-56385800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:56375000-56386000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:56375200-56379600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:56375200-56382800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:56375200-56384600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:56375400-56385400	Weak transcription	Placenta	Placenta
12	chr15:56375600-56386200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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