Variant report

Variant	rs7727576
Chromosome Location	chr5:70710447-70710448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10044572	0.85[EUR][1000 genomes]
rs10077085	0.85[EUR][1000 genomes]
rs10434642	0.88[EUR][1000 genomes]
rs10462368	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10474383	0.88[EUR][1000 genomes]
rs10805884	0.83[EUR][1000 genomes]
rs10942284	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942533	0.90[EUR][1000 genomes]
rs10942682	0.88[EUR][1000 genomes]
rs10942700	0.83[EUR][1000 genomes]
rs10942702	0.85[EUR][1000 genomes]
rs10942705	0.83[EUR][1000 genomes]
rs11743135	0.93[EUR][1000 genomes]
rs11746722	0.85[EUR][1000 genomes]
rs12152748	0.84[EUR][1000 genomes]
rs12514732	0.93[EUR][1000 genomes]
rs13157835	0.85[EUR][1000 genomes]
rs3748043	0.93[EUR][1000 genomes]
rs4062889	0.85[EUR][1000 genomes]
rs4505929	0.85[EUR][1000 genomes]
rs5005863	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6452722	0.92[EUR][1000 genomes]
rs6452900	0.90[EUR][1000 genomes]
rs6453014	0.87[EUR][1000 genomes]
rs6453018	0.88[EUR][1000 genomes]
rs6453035	0.85[EUR][1000 genomes]
rs6872235	0.85[EUR][1000 genomes]
rs6872671	0.84[EUR][1000 genomes]
rs6877289	0.92[EUR][1000 genomes]
rs6877773	0.85[EUR][1000 genomes]
rs6886336	0.88[EUR][1000 genomes]
rs6898471	0.86[EUR][1000 genomes]
rs715747	0.88[EUR][1000 genomes]
rs7378662	0.88[EUR][1000 genomes]
rs7380115	0.85[EUR][1000 genomes]
rs7380280	0.86[EUR][1000 genomes]
rs7444322	0.90[EUR][1000 genomes]
rs7447726	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7448422	0.88[EUR][1000 genomes]
rs7714527	0.90[EUR][1000 genomes]
rs7715648	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721179	0.88[EUR][1000 genomes]
rs7728577	0.90[EUR][1000 genomes]
rs7735544	0.84[EUR][1000 genomes]
rs9968768	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529287	chr5:69732192-70716662	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1033366	chr5:70254883-70710447	Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1031941	chr5:70654060-70710447	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1017385	chr5:70660739-70710447	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1850052	chr5:70674583-70745387	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv528571	chr5:70679626-70767269	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv964892	chr5:70703111-70745996	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7727576	FAM169A	cis	parietal	SCAN
rs7727576	PIK3R1	cis	cerebellum	SCAN
rs7727576	MCCC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70702000-70717400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:70702400-70717600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr5:70707400-70714000	Weak transcription	Liver	Liver
4	chr5:70707600-70716000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr5:70707600-70716400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:70707800-70716400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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