Variant report

Variant	rs10062690
Chromosome Location	chr5:106347551-106347552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr5:106347293-106347608	SK-N-SH_RA	brain:	n/a	n/a
2	GATA3	chr5:106347155-106347767	SK-N-SH	brain:	n/a	n/a
3	EP300	chr5:106347304-106347611	SK-N-SH_RA	brain:	n/a	n/a
4	GATA3	chr5:106347175-106347681	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr5:106347434-106347942	SH-SY5Y	brain:	n/a	n/a
6	CTCF	chr5:106347500-106347650	BE2_C	brain:	n/a	n/a
7	GATA2	chr5:106347235-106347875	SH-SY5Y	brain:	n/a	n/a
8	REST	chr5:106347235-106347613	PFSK-1	brain:	n/a	chr5:106347376-106347389

Variant related genes	Relation type
ENSG00000251027	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10052471	0.80[ASN][1000 genomes]
rs10068963	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10075477	1.00[ASN][1000 genomes]
rs10477875	0.91[ASN][1000 genomes]
rs11744426	1.00[JPT][hapmap]
rs28369477	0.93[ASN][1000 genomes]
rs4073517	0.83[ASN][1000 genomes]
rs4245988	0.88[ASN][1000 genomes]
rs4264929	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4476284	1.00[ASN][1000 genomes]
rs4482891	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4533874	0.98[ASN][1000 genomes]
rs4957682	0.93[ASN][1000 genomes]
rs6862175	0.96[ASN][1000 genomes]
rs6866081	0.82[ASN][1000 genomes]
rs6866693	0.96[ASN][1000 genomes]
rs6867623	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874482	1.00[ASN][1000 genomes]
rs6876240	0.96[ASN][1000 genomes]
rs6885273	0.93[ASN][1000 genomes]
rs7443308	0.80[ASN][1000 genomes]
rs9327985	1.00[ASN][1000 genomes]
rs9327986	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016354	chr5:105752391-106392762	ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
3	nsv830439	chr5:106192038-106383828	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv882679	chr5:106263197-106399718	Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv823170	chr5:106326293-106673695	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv1797744	chr5:106328326-106358541	Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10062690	MAN2A1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106346800-106347800	Enhancers	HSMMtube	muscle
2	chr5:106347200-106347600	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr5:106347200-106347800	Enhancers	Brain Anterior Caudate	brain
4	chr5:106347400-106347800	Enhancers	Skeletal Muscle Female	skeletal muscle

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