Variant report

Variant	rs12823506
Chromosome Location	chr12:50648960-50648961
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50642230..50643787-chr12:50648428..50651289,2	MCF-7	breast:
2	chr12:50477178..50480105-chr12:50648113..50650406,2	K562	blood:
3	chr12:50646771..50649988-chr12:50653700..50656765,4	K562	blood:
4	chr12:50632639..50636668-chr12:50645758..50650000,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000050405	Chromatin interaction
ENSG00000066117	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10467106	0.81[ASN][1000 genomes]
rs10506292	0.89[ASN][1000 genomes]
rs10783344	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783349	0.87[EUR][1000 genomes]
rs10783350	0.84[EUR][1000 genomes]
rs10783353	0.86[ASN][1000 genomes]
rs10876013	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876014	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876015	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876016	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876017	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876018	0.84[EUR][1000 genomes]
rs10876023	0.87[ASN][1000 genomes]
rs10876028	0.87[ASN][1000 genomes]
rs11169314	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169315	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169317	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169319	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169322	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169331	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169332	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169335	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169339	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169345	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169347	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169348	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169349	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169350	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169351	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169357	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169359	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169360	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169367	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169369	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169370	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169371	0.86[EUR][1000 genomes]
rs11169373	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169374	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169375	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169376	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169377	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169379	0.84[EUR][1000 genomes]
rs11169386	0.83[EUR][1000 genomes]
rs11169390	0.87[ASN][1000 genomes]
rs11169391	0.87[ASN][1000 genomes]
rs11169395	0.86[ASN][1000 genomes]
rs11836169	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11838347	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12299669	0.82[ASN][1000 genomes]
rs12299758	0.86[ASN][1000 genomes]
rs12303082	0.87[ASN][1000 genomes]
rs12312177	0.86[ASN][1000 genomes]
rs12422417	0.87[ASN][1000 genomes]
rs12424691	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12424713	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12424876	0.86[ASN][1000 genomes]
rs12425229	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12425705	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12426444	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12811291	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12814094	0.87[ASN][1000 genomes]
rs12821454	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12821504	0.81[EUR][1000 genomes]
rs12828340	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12832940	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1362983	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17124562	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1972611	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984993	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2009072	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2111988	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302900	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2358539	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28628775	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34039674	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34614542	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34825838	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34849043	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34858415	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34894919	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35209607	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35535298	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35663729	0.85[EUR][1000 genomes]
rs35768991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35878271	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35933908	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36017775	0.85[ASN][1000 genomes]
rs3812825	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3861100	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4348979	0.87[ASN][1000 genomes]
rs4421818	0.87[ASN][1000 genomes]
rs4768855	0.86[ASN][1000 genomes]
rs4768872	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768949	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768951	0.83[EUR][1000 genomes]
rs6580730	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6580735	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580736	0.88[EUR][1000 genomes]
rs6580737	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580738	0.88[EUR][1000 genomes]
rs6580739	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6580740	0.86[EUR][1000 genomes]
rs6580741	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6580743	0.84[ASN][1000 genomes]
rs67138019	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7132551	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135777	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71465002	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7295847	0.89[ASN][1000 genomes]
rs7296291	0.89[ASN][1000 genomes]
rs7301186	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7301189	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7302363	0.87[ASN][1000 genomes]
rs7304445	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7305995	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7308095	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7308885	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7310541	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7311378	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7311491	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7311973	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7312252	0.89[ASN][1000 genomes]
rs7314465	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7315871	0.86[EUR][1000 genomes]
rs7315955	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7399343	0.84[EUR][1000 genomes]
rs7485486	0.86[EUR][1000 genomes]
rs7486747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488682	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7489214	0.84[EUR][1000 genomes]
rs7953953	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956468	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972824	0.83[ASN][1000 genomes]
rs7974648	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7979830	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980911	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9668187	0.86[ASN][1000 genomes]
rs9705460	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9739363	0.87[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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12823506	CERS5	cis	Nerve Tibial	GTEx
rs12823506	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs12823506	ATF1	cis	Artery Tibial	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50616800-50651800	Weak transcription	Brain Anterior Caudate	brain
2	chr12:50633200-50651200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:50636200-50651200	Weak transcription	Fetal Kidney	kidney
4	chr12:50636600-50651400	Weak transcription	Gastric	stomach
5	chr12:50636600-50651800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:50639000-50651600	Weak transcription	Fetal Lung	lung
7	chr12:50640400-50651200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:50641000-50662000	Weak transcription	Brain Germinal Matrix	brain
9	chr12:50641200-50653200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:50641400-50659600	Weak transcription	Esophagus	oesophagus
11	chr12:50641800-50651200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:50641800-50651200	Weak transcription	Left Ventricle	heart
13	chr12:50641800-50651200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:50641800-50651800	Weak transcription	Fetal Stomach	stomach
15	chr12:50641800-50651800	Weak transcription	Right Ventricle	heart
16	chr12:50641800-50652000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:50642600-50651200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr12:50642600-50652000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:50642800-50649000	Weak transcription	Aorta	Aorta
20	chr12:50642800-50651200	Weak transcription	Brain Angular Gyrus	brain
21	chr12:50643000-50649400	Enhancers	Fetal Intestine Large	intestine
22	chr12:50643000-50651000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:50643000-50651200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:50643200-50651000	Weak transcription	Adipose Nuclei	Adipose
25	chr12:50643600-50649200	Enhancers	Stomach Mucosa	stomach
26	chr12:50643800-50651000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:50643800-50651200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:50643800-50651400	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:50644000-50651000	Weak transcription	Psoas Muscle	Psoas
30	chr12:50644000-50651000	Weak transcription	Right Atrium	heart
31	chr12:50644000-50651200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:50644000-50652000	Weak transcription	Ovary	ovary
33	chr12:50644200-50650000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:50644400-50650000	Enhancers	Fetal Intestine Small	intestine
35	chr12:50644800-50649200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:50645000-50649200	Enhancers	NHEK	skin
37	chr12:50646000-50650400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:50646000-50650800	Weak transcription	HSMM	muscle
39	chr12:50646000-50651000	Weak transcription	HSMMtube	muscle
40	chr12:50646000-50651200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:50646000-50651200	Weak transcription	Osteobl	bone
42	chr12:50646000-50651400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:50646000-50651400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:50646200-50651000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:50646200-50651000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:50646800-50649200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:50646800-50649200	Enhancers	HepG2	liver
48	chr12:50647400-50649000	Enhancers	Primary B cells from peripheral blood	blood
49	chr12:50647400-50649800	Enhancers	Placenta	Placenta
50	chr12:50647800-50649200	Enhancers	HMEC	breast

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