Variant report

Variant	rs33565
Chromosome Location	chr5:112305313-112305314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:112256092..112257666-chr5:112304099..112305751,2	MCF-7	breast:
2	chr5:112263017..112264947-chr5:112304699..112307617,2	MCF-7	breast:
3	chr5:112298220..112301576-chr5:112303525..112306248,4	K562	blood:
4	chr5:112304286..112307784-chr5:112309316..112313122,5	MCF-7	breast:
5	chr5:112295383..112297610-chr5:112302677..112305586,2	K562	blood:
6	chr5:112299891..112302551-chr5:112304057..112307148,4	K562	blood:

Variant related genes	Relation type
ENSG00000172795	Chromatin interaction
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10059599	0.94[JPT][hapmap]
rs12516502	0.94[JPT][hapmap]
rs12719155	0.92[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2052484	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2080896	0.94[JPT][hapmap]
rs2112452	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2112453	0.94[JPT][hapmap]
rs33547	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs33550	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs33553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs33563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3733969	0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3857433	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs4260660	0.88[JPT][hapmap]
rs4705530	0.85[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs4705533	0.94[JPT][hapmap]
rs4705743	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4705746	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs4705754	0.93[JPT][hapmap]
rs6594659	0.88[JPT][hapmap]
rs7447818	0.94[JPT][hapmap]
rs7718810	0.94[JPT][hapmap]
rs878073	0.94[JPT][hapmap]
rs878076	0.94[JPT][hapmap]
rs882253	0.94[JPT][hapmap]
rs888844	0.91[JPT][hapmap]
rs9326869	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs959949	0.93[JPT][hapmap]

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	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs33565	MAN2A1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112294000-112311800	Weak transcription	Right Atrium	heart
2	chr5:112298200-112311800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:112300000-112305600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr5:112300000-112307000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:112300200-112311400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:112302000-112306200	Enhancers	Placenta	Placenta
7	chr5:112303600-112305600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:112303600-112305800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:112303800-112305800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr5:112304200-112305400	Enhancers	GM12878-XiMat	blood
11	chr5:112304200-112305600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:112304200-112305600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr5:112304200-112305600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr5:112304200-112306000	Enhancers	H1 Cell Line	embryonic stem cell
15	chr5:112304400-112305600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr5:112304400-112305800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr5:112304400-112309400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:112304600-112305600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:112304600-112305600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr5:112304600-112305600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr5:112304600-112305600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:112304600-112305600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:112304600-112305800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:112304600-112306000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr5:112304600-112306000	Enhancers	HepG2	liver
26	chr5:112304800-112305400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:112304800-112305400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr5:112304800-112305600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:112305000-112305600	Enhancers	Hela-S3	cervix
30	chr5:112305000-112305800	Flanking Active TSS	A549	lung
31	chr5:112305000-112305800	Enhancers	HUVEC	blood vessel
32	chr5:112305000-112306000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr5:112305200-112305400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr5:112305200-112305600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr5:112305200-112305600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:112305200-112305600	Flanking Active TSS	K562	blood
37	chr5:112305200-112305600	Enhancers	NH-A	brain
38	chr5:112305200-112305800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr5:112305200-112305800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:112305200-112305800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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