Variant report

Variant	rs9225
Chromosome Location	chr2:47086112-47086113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:47080558..47082163-chr2:47086057..47089027,2	K562	blood:
2	chr2:47085558..47087173-chr2:47093819..47096173,2	K562	blood:
3	chr2:47081928..47083948-chr2:47085603..47087171,2	MCF-7	breast:
4	chr2:47084849..47086981-chr2:47087555..47090038,3	K562	blood:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC016722.1.1-1	chr2:47085219-47086145	XLOC_001458
2	lnc-AC016722.1.1-1	chr2:47085225-47086145	XLOC_001458
3	lnc-AC016722.1.1-1	chr2:47085219-47086117	XLOC_001458
4	lnc-AC016722.1.1-1	chr2:47085225-47086117	XLOC_001458
5	lnc-AC016722.1.1-1	chr2:47085225-47086146	NONHSAT070529

No data

Variant related genes	Relation type
ENSG00000239332	Chromatin interaction
ENSG00000226548	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10170987	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10177555	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10177751	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10183609	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11125096	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125097	0.87[ASN][1000 genomes]
rs11687883	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11689551	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12614366	0.83[MEX][hapmap]
rs2166478	0.81[CEU][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2278711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278712	0.81[ASN][1000 genomes]
rs34392693	0.81[ASN][1000 genomes]
rs4953433	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6759066	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs935372	0.83[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs935379	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9225	PREPL	cis	cerebellum	SCAN
rs9225	FBXO11	cis	cerebellum	SCAN
rs9225	KCNK12	cis	parietal	SCAN
rs9225	ABCG8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47077200-47086200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:47080800-47103600	Enhancers	Placenta	Placenta
3	chr2:47081200-47087200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:47081400-47086400	Enhancers	HMEC	breast
5	chr2:47081400-47086600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:47081400-47087200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:47081400-47087800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:47081400-47091000	Enhancers	NHDF-Ad	bronchial
9	chr2:47081600-47087800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr2:47082200-47089000	Weak transcription	Colonic Mucosa	Colon
11	chr2:47083000-47086200	Weak transcription	Adipose Nuclei	Adipose
12	chr2:47083200-47088600	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:47083800-47086200	Enhancers	A549	lung
14	chr2:47084000-47086800	Weak transcription	Spleen	Spleen
15	chr2:47084000-47088400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:47084000-47088800	Weak transcription	Right Ventricle	heart
17	chr2:47084000-47093200	Weak transcription	Ovary	ovary
18	chr2:47084000-47093600	Weak transcription	Right Atrium	heart
19	chr2:47084200-47087200	Enhancers	Osteobl	bone
20	chr2:47084200-47088400	Weak transcription	Left Ventricle	heart
21	chr2:47084800-47087000	Enhancers	HSMM	muscle
22	chr2:47084800-47088200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr2:47085000-47086800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:47085000-47086800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:47085000-47086800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:47085000-47087000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:47085000-47090400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:47085200-47086200	Enhancers	Colon Smooth Muscle	Colon
29	chr2:47085200-47086400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr2:47085200-47086400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:47085200-47086600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:47085200-47086800	Enhancers	HSMMtube	muscle
33	chr2:47085600-47087200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:47085800-47086400	Weak transcription	Lung	lung
35	chr2:47085800-47087200	Enhancers	NHLF	lung
36	chr2:47085800-47087600	Weak transcription	Fetal Lung	lung
37	chr2:47085800-47089400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:47086000-47086800	Enhancers	NH-A	brain
39	chr2:47086000-47088600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:47086000-47091200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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