Variant report

Variant	rs1472225
Chromosome Location	chr1:212402564-212402565
allele	A/G
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	FOXA1	chr1:212401777-212402601	HepG2	liver:	n/a	n/a
2	FOXA2	chr1:212401496-212402652	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212401784..212403984-chr1:212456649..212458602,2	K562	blood:

Variant related genes	Relation type
ENSG00000226251	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10779576	0.87[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10863949	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11119881	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1873298	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1962127	0.92[ASN][1000 genomes]
rs1967115	0.95[ASN][1000 genomes]
rs2358453	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2921128	0.83[CHB][hapmap]
rs4951578	0.95[ASN][1000 genomes]
rs4951584	0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs6678627	0.86[ASN][1000 genomes]
rs7516619	0.82[EUR][1000 genomes]
rs7548606	0.96[ASN][1000 genomes]
rs792433	0.82[CHB][hapmap]
rs792443	0.83[CHB][hapmap]
rs903123	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1472225	PPP2R5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212392600-212404800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:212398800-212402600	Enhancers	Stomach Mucosa	stomach
3	chr1:212399000-212403200	Enhancers	Fetal Heart	heart
4	chr1:212399400-212405200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr1:212399600-212403200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:212399600-212404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:212399600-212404800	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:212399800-212403200	Weak transcription	Right Ventricle	heart
9	chr1:212399800-212403800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:212399800-212405200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr1:212399800-212406600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:212399800-212407800	Weak transcription	Brain Anterior Caudate	brain
13	chr1:212400000-212404800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:212400000-212405000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:212400000-212405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:212400000-212405200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:212400000-212405200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:212400000-212405200	Weak transcription	Fetal Thymus	thymus
19	chr1:212400000-212407600	Weak transcription	Spleen	Spleen
20	chr1:212400000-212407800	Weak transcription	Right Atrium	heart
21	chr1:212400000-212407800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:212400200-212405400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:212400200-212406800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:212400600-212404200	Enhancers	Pancreas	Pancrea
25	chr1:212400800-212402800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:212401000-212402600	Enhancers	NHDF-Ad	bronchial
27	chr1:212401200-212403000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:212401200-212404200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:212401400-212403200	Weak transcription	Small Intestine	intestine
30	chr1:212401400-212408400	Weak transcription	Lung	lung
31	chr1:212401600-212402600	Enhancers	Fetal Kidney	kidney
32	chr1:212401600-212402800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:212401600-212403400	Enhancers	Fetal Intestine Large	intestine
34	chr1:212401600-212403400	Enhancers	Fetal Intestine Small	intestine
35	chr1:212401600-212405000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:212401800-212409000	Weak transcription	Gastric	stomach
37	chr1:212402400-212402600	Flanking Active TSS	Liver	Liver
38	chr1:212402400-212402800	Enhancers	A549	lung
39	chr1:212402400-212403800	Enhancers	HepG2	liver
40	chr1:212402400-212404800	Weak transcription	Left Ventricle	heart
41	chr1:212402400-212407800	Weak transcription	Rectal Mucosa Donor 31	rectum

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