Variant report

Variant	rs4957679
Chromosome Location	chr5:106303607-106303608
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10052471	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10062690	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10068963	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10075477	0.85[AMR][1000 genomes]
rs10477875	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10479391	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744426	1.00[JPT][hapmap]
rs12054932	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12653426	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369477	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4073517	0.81[AMR][1000 genomes]
rs4262090	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4264929	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap]
rs4351137	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4382150	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4476284	0.85[AMR][1000 genomes]
rs4533874	0.85[AMR][1000 genomes]
rs6866081	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6866693	0.82[AMR][1000 genomes]
rs6874482	0.85[AMR][1000 genomes]
rs6880364	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885273	0.82[AMR][1000 genomes]
rs6893146	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7443308	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9327986	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1841017	chr5:106299280-106325865	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4957679	MAN2A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106295800-106309400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:106298800-106308400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:106299800-106305400	Weak transcription	Psoas Muscle	Psoas
4	chr5:106300200-106309000	Weak transcription	Fetal Heart	heart
5	chr5:106300800-106308200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:106302400-106308400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr5:106302400-106314200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:106302600-106308200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:106302800-106304800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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