Variant report

Variant	rs7485673
Chromosome Location	chr12:105443966-105443967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10861314	0.92[ASN][1000 genomes]
rs10861315	0.92[ASN][1000 genomes]
rs10861316	0.92[ASN][1000 genomes]
rs11112320	0.81[AFR][1000 genomes]
rs11112322	0.81[AFR][1000 genomes]
rs11112330	0.92[ASN][1000 genomes]
rs12227643	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12231561	0.92[ASN][1000 genomes]
rs12231563	0.92[ASN][1000 genomes]
rs4964120	0.89[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs4964310	0.84[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs4964314	0.92[ASN][1000 genomes]
rs4964315	0.92[ASN][1000 genomes]
rs4964316	0.94[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs4964317	0.92[ASN][1000 genomes]
rs7133683	0.88[ASN][1000 genomes]
rs7133801	0.92[ASN][1000 genomes]
rs7134259	0.92[ASN][1000 genomes]
rs7313529	0.84[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs7315784	0.88[ASN][1000 genomes]
rs7316236	0.88[ASN][1000 genomes]
rs7956169	0.92[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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7485673	TCP11L2	cis	parietal	SCAN
rs7485673	C12orf45	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105409200-105446800	Weak transcription	Left Ventricle	heart
2	chr12:105409400-105465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr12:105410800-105446400	Weak transcription	K562	blood
4	chr12:105413000-105445000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:105413000-105476800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:105413200-105457800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr12:105414800-105447200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:105414800-105454000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:105420000-105477000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:105420400-105448600	Weak transcription	Ovary	ovary
11	chr12:105420600-105447000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:105423200-105459400	Weak transcription	Lung	lung
13	chr12:105431000-105446800	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:105431400-105445000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:105431400-105461600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:105431800-105454800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:105432200-105454600	Weak transcription	NHEK	skin
18	chr12:105434000-105453000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:105435200-105453600	Weak transcription	Fetal Stomach	stomach
20	chr12:105435400-105445000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:105435400-105445000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:105435600-105444800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:105435600-105446200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:105435600-105467400	Weak transcription	Brain Substantia Nigra	brain
25	chr12:105435800-105446600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:105436800-105445400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:105436800-105446600	Strong transcription	Osteobl	bone
28	chr12:105437200-105448600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:105439600-105446800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:105439800-105446800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:105440200-105445800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:105440200-105449800	Strong transcription	HSMMtube	muscle
33	chr12:105440400-105444200	Strong transcription	NH-A	brain
34	chr12:105440400-105445400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:105440400-105445400	Strong transcription	HMEC	breast
36	chr12:105440400-105446000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr12:105440400-105446600	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr12:105440400-105446800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:105440400-105448600	Strong transcription	HSMM	muscle
40	chr12:105440600-105444200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:105440600-105444400	Strong transcription	Adipose Nuclei	Adipose
42	chr12:105440800-105444200	Strong transcription	Fetal Brain Female	brain
43	chr12:105441200-105445400	Strong transcription	NHDF-Ad	bronchial
44	chr12:105441200-105446800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:105441200-105477000	Weak transcription	Gastric	stomach
46	chr12:105441400-105446800	Weak transcription	Placenta	Placenta
47	chr12:105441400-105453400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:105441400-105454800	Weak transcription	Pancreas	Pancrea
49	chr12:105441600-105448800	Weak transcription	A549	lung
50	chr12:105441600-105458200	Weak transcription	Right Ventricle	heart

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