Variant report

Variant	rs4262090
Chromosome Location	chr5:106313599-106313600
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10052471	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10062690	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10068963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10075477	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10477875	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10479391	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10479392	0.81[ASN][1000 genomes]
rs11744426	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs12054932	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12653426	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28369477	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4073517	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4264929	0.85[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap]
rs4351137	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382150	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4476284	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4533874	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4632787	0.80[ASN][1000 genomes]
rs4957679	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6866081	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6866693	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6874482	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6880364	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6885273	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6893146	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7443308	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9327985	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9327986	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
6	esv1795812	chr5:106308008-106326299	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
7	esv1799346	chr5:106308008-106326299	Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
8	esv1815884	chr5:106308008-106326299	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
9	esv1843510	chr5:106308008-106326299	Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
10	esv1850520	chr5:106308008-106326299	Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
11	esv1815273	chr5:106308008-106326475	Enhancers Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
12	esv1799129	chr5:106311248-106326299	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
13	esv1802235	chr5:106311248-106326299	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
14	esv1817753	chr5:106311248-106326299	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	n/a
15	esv1844969	chr5:106311248-106326299	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS 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
rs4262090	MAN2A1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106302400-106314200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:106308000-106313600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr5:106308800-106314200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:106312200-106314000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr5:106312400-106313800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:106312600-106314400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr5:106312600-106314400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:106312800-106314200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr5:106313000-106314000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:106313200-106313800	Enhancers	Colon Smooth Muscle	Colon
11	chr5:106313200-106314000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:106313200-106314200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr5:106313200-106314400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr5:106313200-106314400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell

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