Variant report

Variant	rs4774231
Chromosome Location	chr15:56368655-56368656
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11629483	0.86[EUR][1000 genomes]
rs11631191	0.86[EUR][1000 genomes]
rs12905899	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs12907263	0.89[EUR][1000 genomes]
rs12911094	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911427	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs12914260	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1372753	0.84[EUR][1000 genomes]
rs1442640	0.91[EUR][1000 genomes]
rs2119937	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2460650	0.84[CEU][hapmap]
rs2682051	0.84[CEU][hapmap]
rs2682054	0.85[CEU][hapmap]
rs2682059	0.81[CEU][hapmap]
rs2713924	0.85[CEU][hapmap]
rs2713933	0.85[CEU][hapmap]
rs2713936	0.84[CEU][hapmap]
rs2713938	0.81[EUR][1000 genomes]
rs2713941	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2718934	0.84[CEU][hapmap]
rs2718941	0.85[CEU][hapmap]
rs2725870	0.83[EUR][1000 genomes]
rs34044869	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34144128	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34224072	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34386737	0.90[EUR][1000 genomes]
rs34777702	0.85[ASN][1000 genomes]
rs34979470	0.85[ASN][1000 genomes]
rs35082998	0.95[EUR][1000 genomes]
rs35722267	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35749329	0.86[EUR][1000 genomes]
rs35972806	0.84[EUR][1000 genomes]
rs4310791	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs4310792	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs4774232	0.84[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4774847	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59432349	0.86[EUR][1000 genomes]
rs62044082	0.87[EUR][1000 genomes]
rs62044110	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62044111	0.93[EUR][1000 genomes]
rs6493835	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7165270	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7168319	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7174823	0.85[EUR][1000 genomes]
rs7175745	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7176107	0.88[CEU][hapmap];0.95[YRI][hapmap]
rs7179706	0.89[ASN][1000 genomes]
rs7183363	0.95[ASN][1000 genomes]
rs7496025	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8024031	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8028353	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8029114	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8032242	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8033653	0.94[EUR][1000 genomes]
rs9672886	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs9672928	0.84[EUR][1000 genomes]

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	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
4	nsv522888	chr15:56362968-56369124	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4774231	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs4774231	FLJ12994	cis	multi-tissue	Pritchard
rs4774231	RFX7	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:5 , 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	chr15:56366400-56370600	Enhancers	Fetal Brain Male	brain
3	chr15:56367600-56369200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:56368000-56369800	Enhancers	Fetal Brain Female	brain
5	chr15:56368600-56370200	Enhancers	Brain Germinal Matrix	brain

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