Variant report

Variant	rs11043275
Chromosome Location	chr12:122402723-122402724
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122400159..122402861-chr12:122407797..122409946,2	MCF-7	breast:
2	chr12:122393592..122395779-chr12:122400656..122403431,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11043271	0.83[EUR][1000 genomes]
rs11043278	0.83[EUR][1000 genomes]
rs1154514	0.80[EUR][1000 genomes]
rs11612028	0.83[EUR][1000 genomes]
rs1169070	0.83[EUR][1000 genomes]
rs1169071	0.83[EUR][1000 genomes]
rs12822775	0.83[EUR][1000 genomes]
rs12829688	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1720033	0.83[EUR][1000 genomes]
rs1720037	0.81[EUR][1000 genomes]
rs1824949	0.95[ASN][1000 genomes]
rs2004863	0.85[ASN][1000 genomes]
rs2004864	0.85[ASN][1000 genomes]
rs2076860	0.85[ASN][1000 genomes]
rs3741581	0.85[ASN][1000 genomes]
rs55778445	0.95[ASN][1000 genomes]
rs58025403	0.85[ASN][1000 genomes]
rs58026220	0.95[ASN][1000 genomes]
rs58158474	0.85[ASN][1000 genomes]
rs58516770	0.85[ASN][1000 genomes]
rs59116149	0.85[ASN][1000 genomes]
rs59178789	0.85[ASN][1000 genomes]
rs60620185	0.95[ASN][1000 genomes]
rs7138299	0.95[ASN][1000 genomes]
rs7138556	0.85[ASN][1000 genomes]
rs7294535	0.95[ASN][1000 genomes]
rs7294829	0.85[ASN][1000 genomes]
rs7314352	0.95[ASN][1000 genomes]
rs830125	0.95[ASN][1000 genomes]
rs872781	0.85[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11043275	PSMD9	cis	brain	BrainEAC

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122363600-122408000	Weak transcription	Right Ventricle	heart
2	chr12:122365800-122405000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:122370600-122403200	Weak transcription	Fetal Kidney	kidney
4	chr12:122374000-122402800	Weak transcription	HSMM	muscle
5	chr12:122374000-122405600	Weak transcription	Adipose Nuclei	Adipose
6	chr12:122375800-122415800	Weak transcription	Liver	Liver
7	chr12:122376000-122413000	Weak transcription	Aorta	Aorta
8	chr12:122377400-122406200	Weak transcription	Thymus	Thymus
9	chr12:122380800-122405800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:122381000-122405800	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:122391400-122410800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:122391600-122402800	Weak transcription	A549	lung
13	chr12:122391600-122405600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:122391800-122410800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:122394000-122429800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:122394200-122402800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:122394200-122407600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:122394200-122411000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:122394200-122411200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:122396000-122408000	Weak transcription	Fetal Intestine Small	intestine
21	chr12:122396600-122408200	Weak transcription	Fetal Brain Female	brain
22	chr12:122396600-122439200	Weak transcription	Brain Anterior Caudate	brain
23	chr12:122396800-122402800	Weak transcription	NH-A	brain
24	chr12:122396800-122410800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:122397200-122403000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:122397200-122406000	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:122397200-122408400	Weak transcription	Brain Substantia Nigra	brain
28	chr12:122397600-122403000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:122397600-122406000	Weak transcription	Esophagus	oesophagus
30	chr12:122398800-122406200	Weak transcription	Fetal Thymus	thymus
31	chr12:122399000-122411000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:122399000-122411000	Weak transcription	Gastric	stomach
33	chr12:122400200-122404800	Weak transcription	K562	blood
34	chr12:122400200-122408200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:122400600-122402800	Weak transcription	HMEC	breast
36	chr12:122400800-122402800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:122401400-122408200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:122401600-122403200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:122401600-122404000	Enhancers	Osteobl	bone
40	chr12:122401800-122404000	Enhancers	Muscle Satellite Cultured Cells	--
41	chr12:122401800-122404000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:122401800-122404000	Genic enhancers	NHEK	skin
43	chr12:122401800-122404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:122402000-122404800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:122402000-122405800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:122402000-122405800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:122402000-122406000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:122402000-122408800	Weak transcription	Pancreas	Pancrea
49	chr12:122402000-122412400	Weak transcription	Ovary	ovary
50	chr12:122402000-122412800	Weak transcription	Spleen	Spleen

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