Variant report

Variant	rs1532365
Chromosome Location	chr12:49204421-49204422
allele	C/T
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	MAZ	chr12:49203806-49206443	IMR90	lung:	n/a	n/a
2	RCOR1	chr12:49204192-49206087	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49203980..49213270-chr12:49239370..49250118,15	MCF-7	breast:
2	chr12:49182132..49185770-chr12:49202933..49205906,3	MCF-7	breast:
3	chr12:49073658..49078597-chr12:49201352..49212442,12	MCF-7	breast:

Variant related genes	Relation type
CACNB3	TF binding region
ENSG00000257660	Chromatin interaction
ENSG00000174233	Chromatin interaction
ENSG00000139620	Chromatin interaction
ENSG00000174243	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10875876	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875877	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2070615	0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2446989	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2446992	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2453468	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2453469	0.82[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.88[MKK][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2453478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453479	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2860360	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2926803	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2926804	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3101344	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760643	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6580695	0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs903568	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs931570	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9706255	0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv826363	chr12:49177227-49250989	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1532365	AMIGO2	cis	parietal	SCAN
rs1532365	GPD1	cis	parietal	SCAN
rs1532365	AQP2	cis	cerebellum	SCAN
rs1532365	DNAJC22	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49201200-49207600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:49201600-49207600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:49203000-49204600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:49203600-49207600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:49203800-49205600	Enhancers	Fetal Kidney	kidney
6	chr12:49203800-49205800	Enhancers	Stomach Smooth Muscle	stomach
7	chr12:49204000-49204600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:49204000-49204600	Enhancers	Osteobl	bone
9	chr12:49204000-49204800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:49204000-49205400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:49204000-49205600	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr12:49204000-49205800	Enhancers	Fetal Intestine Large	intestine
13	chr12:49204000-49205800	Enhancers	Fetal Lung	lung
14	chr12:49204000-49206400	Enhancers	Fetal Intestine Small	intestine
15	chr12:49204000-49207200	Enhancers	Ovary	ovary
16	chr12:49204000-49207400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:49204200-49204800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:49204200-49204800	Enhancers	A549	lung
19	chr12:49204200-49205200	Flanking Active TSS	HepG2	liver
20	chr12:49204200-49205400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:49204200-49205400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:49204200-49205400	Enhancers	Stomach Mucosa	stomach
23	chr12:49204200-49205800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:49204200-49206000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr12:49204200-49206200	Enhancers	Duodenum Mucosa	Duodenum
26	chr12:49204200-49206200	Enhancers	HSMMtube	muscle
27	chr12:49204200-49206400	Enhancers	Fetal Stomach	stomach
28	chr12:49204200-49206600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:49204200-49206800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:49204200-49207600	Enhancers	Fetal Muscle Trunk	muscle
31	chr12:49204200-49207600	Enhancers	Placenta	Placenta
32	chr12:49204400-49204600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:49204400-49204600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr12:49204400-49204600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:49204400-49204600	Enhancers	Spleen	Spleen
36	chr12:49204400-49204600	Enhancers	NH-A	brain
37	chr12:49204400-49204800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
38	chr12:49204400-49204800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:49204400-49205000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
40	chr12:49204400-49205000	Flanking Active TSS	NHLF	lung
41	chr12:49204400-49205200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr12:49204400-49205600	Enhancers	Gastric	stomach
43	chr12:49204400-49205800	Enhancers	Colonic Mucosa	Colon
44	chr12:49204400-49206200	Enhancers	Fetal Muscle Leg	muscle
45	chr12:49204400-49206200	Enhancers	Lung	lung
46	chr12:49204400-49206200	Enhancers	NHDF-Ad	bronchial
47	chr12:49204400-49206600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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