Variant report

Variant	rs57955254
Chromosome Location	chr12:42787053-42787054
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42778808..42780511-chr12:42787009..42789795,2	K562	blood:
2	chr12:42785926..42787978-chr12:42791013..42793479,2	K562	blood:

Variant related genes	Relation type
ENSG00000199886	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11829039	1.00[EUR][1000 genomes]
rs11829542	1.00[EUR][1000 genomes]
rs11830248	1.00[EUR][1000 genomes]
rs11830386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11831464	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11832196	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11832840	1.00[EUR][1000 genomes]
rs11833011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11833109	1.00[EUR][1000 genomes]
rs11833381	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11834665	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11837839	1.00[EUR][1000 genomes]
rs17091023	1.00[EUR][1000 genomes]
rs2406968	1.00[EUR][1000 genomes]
rs56691329	1.00[EUR][1000 genomes]
rs57490344	1.00[EUR][1000 genomes]
rs57647260	1.00[EUR][1000 genomes]
rs58229270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58676357	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59190545	1.00[EUR][1000 genomes]
rs59577937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59645146	1.00[EUR][1000 genomes]
rs60314019	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60982601	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61067658	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7299386	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73270269	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73270275	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73270279	1.00[EUR][1000 genomes]
rs73270293	1.00[EUR][1000 genomes]
rs73272004	1.00[EUR][1000 genomes]
rs73272008	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272013	1.00[EUR][1000 genomes]
rs73272046	1.00[EUR][1000 genomes]
rs73272047	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73272050	1.00[EUR][1000 genomes]
rs73272072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272073	1.00[EUR][1000 genomes]
rs73272080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73272101	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73273911	1.00[EUR][1000 genomes]
rs73273932	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73273975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73277820	1.00[EUR][1000 genomes]
rs73281851	1.00[EUR][1000 genomes]
rs73281860	1.00[EUR][1000 genomes]
rs73281880	1.00[EUR][1000 genomes]
rs73281886	1.00[EUR][1000 genomes]
rs73281894	1.00[EUR][1000 genomes]
rs73283707	1.00[EUR][1000 genomes]
rs73283734	1.00[EUR][1000 genomes]
rs73283759	1.00[EUR][1000 genomes]
rs73283792	1.00[EUR][1000 genomes]
rs73283799	1.00[EUR][1000 genomes]
rs73285617	1.00[EUR][1000 genomes]
rs73285619	1.00[EUR][1000 genomes]
rs73285621	1.00[EUR][1000 genomes]
rs73285641	1.00[EUR][1000 genomes]
rs73285662	1.00[EUR][1000 genomes]
rs73285670	1.00[EUR][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:112 , 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	chr12:42722000-42793200	Weak transcription	Fetal Kidney	kidney
7	chr12:42732200-42794400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:42733400-42796800	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:42738000-42787400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:42738200-42823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:42763800-42804200	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:42766200-42796800	Weak transcription	Aorta	Aorta
13	chr12:42767200-42836200	Weak transcription	Esophagus	oesophagus
14	chr12:42769800-42794200	Weak transcription	Left Ventricle	heart
15	chr12:42770000-42794000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:42770200-42815800	Weak transcription	Fetal Lung	lung
17	chr12:42770400-42790400	Weak transcription	HUVEC	blood vessel
18	chr12:42770400-42795400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:42770400-42816600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:42770600-42787200	Weak transcription	GM12878-XiMat	blood
21	chr12:42771000-42792600	Weak transcription	HepG2	liver
22	chr12:42771000-42795000	Weak transcription	HSMMtube	muscle
23	chr12:42771000-42796800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:42771000-42799000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr12:42771200-42794400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:42771200-42801000	Weak transcription	NH-A	brain
27	chr12:42771600-42793400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:42771800-42803000	Weak transcription	Brain Anterior Caudate	brain
29	chr12:42775800-42790200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:42776000-42792000	Weak transcription	HMEC	breast
31	chr12:42776200-42795400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr12:42776400-42787400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:42776400-42789400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:42777000-42802600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr12:42778000-42798200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr12:42778200-42788600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr12:42778400-42789800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr12:42779000-42798400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:42779400-42789000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:42779400-42797800	Weak transcription	Brain Germinal Matrix	brain
41	chr12:42779800-42795000	Weak transcription	Osteobl	bone
42	chr12:42780200-42802800	Weak transcription	Right Ventricle	heart
43	chr12:42780200-42836000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr12:42780400-42788600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr12:42780400-42794800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr12:42780400-42795000	Weak transcription	NHEK	skin
47	chr12:42780400-42804200	Weak transcription	K562	blood
48	chr12:42780400-42811200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:42780600-42788200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:42780800-42789600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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