Variant report

Variant	rs73124406
Chromosome Location	chr12:42794353-42794354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42791162..42793820-chr12:42794033..42796036,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199886	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10160853	0.83[ASN][1000 genomes]
rs1037401	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10506175	0.83[ASN][1000 genomes]
rs11181373	0.83[ASN][1000 genomes]
rs1139095	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830387	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832838	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297206	0.85[ASN][1000 genomes]
rs12300188	0.85[ASN][1000 genomes]
rs12312515	0.83[ASN][1000 genomes]
rs12317772	0.83[ASN][1000 genomes]
rs17091061	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17091083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091094	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091117	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17091138	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091141	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091163	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091193	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091220	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17091226	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17121217	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1962526	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987127	0.88[ASN][1000 genomes]
rs2305423	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406676	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406677	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747559	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810787	0.87[EUR][1000 genomes]
rs3911246	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57447201	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57653125	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58594062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59402225	0.95[EUR][1000 genomes]
rs59423833	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59501472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60092940	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60287587	0.83[ASN][1000 genomes]
rs60598518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60659836	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67128387	0.83[EUR][1000 genomes]
rs73114487	0.83[ASN][1000 genomes]
rs73116432	0.88[ASN][1000 genomes]
rs73116492	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73118486	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73118500	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73120410	0.95[EUR][1000 genomes]
rs73120468	0.95[EUR][1000 genomes]
rs73120476	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73120499	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73124495	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73126404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73126407	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73126412	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73126433	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73126453	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7961228	0.88[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	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42721600-42800800	Weak transcription	Psoas Muscle	Psoas
3	chr12:42721600-42803600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:42721800-42797000	Weak transcription	NHLF	lung
5	chr12:42721800-42803600	Weak transcription	Gastric	stomach
6	chr12:42732200-42794400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:42733400-42796800	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:42738200-42823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:42763800-42804200	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:42766200-42796800	Weak transcription	Aorta	Aorta
11	chr12:42767200-42836200	Weak transcription	Esophagus	oesophagus
12	chr12:42770200-42815800	Weak transcription	Fetal Lung	lung
13	chr12:42770400-42795400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:42770400-42816600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:42771000-42795000	Weak transcription	HSMMtube	muscle
16	chr12:42771000-42796800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:42771000-42799000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:42771200-42794400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:42771200-42801000	Weak transcription	NH-A	brain
20	chr12:42771800-42803000	Weak transcription	Brain Anterior Caudate	brain
21	chr12:42776200-42795400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:42777000-42802600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:42778000-42798200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:42779000-42798400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:42779400-42797800	Weak transcription	Brain Germinal Matrix	brain
26	chr12:42779800-42795000	Weak transcription	Osteobl	bone
27	chr12:42780200-42802800	Weak transcription	Right Ventricle	heart
28	chr12:42780200-42836000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:42780400-42794800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:42780400-42795000	Weak transcription	NHEK	skin
31	chr12:42780400-42804200	Weak transcription	K562	blood
32	chr12:42780400-42811200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr12:42782000-42802000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:42782800-42797000	Weak transcription	Ovary	ovary
35	chr12:42782800-42803400	Weak transcription	Spleen	Spleen
36	chr12:42782800-42804200	Weak transcription	Fetal Brain Female	brain
37	chr12:42782800-42807200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:42783000-42836000	Weak transcription	Lung	lung
39	chr12:42783200-42795200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:42784000-42795200	Weak transcription	A549	lung
41	chr12:42784400-42794400	Weak transcription	Thymus	Thymus
42	chr12:42784400-42795000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:42785400-42836000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:42786600-42795200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:42788400-42796800	Weak transcription	HSMM	muscle
46	chr12:42789600-42795400	Weak transcription	Fetal Brain Male	brain
47	chr12:42789600-42812200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:42789600-42836200	Weak transcription	Pancreas	Pancrea
49	chr12:42790600-42802600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:42790600-42803800	Weak transcription	Colonic Mucosa	Colon

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