Variant report

Variant	rs55771933
Chromosome Location	chr12:31610806-31610807
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	chr12:31610070..31611631-chr12:31742712..31744652,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255867	Chromatin interaction
ENSG00000170456	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1038066	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12809140	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12812075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812141	1.00[ASN][1000 genomes]
rs12816170	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816386	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818749	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12819062	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12820294	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12821808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822601	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825207	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12826193	0.87[EUR][1000 genomes]
rs12831480	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17497517	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17497656	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17497998	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1879399	1.00[ASN][1000 genomes]
rs2126897	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34007930	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34094545	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34184789	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34271764	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34308937	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34450466	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585237	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34642866	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34667511	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34949976	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34955459	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34986122	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35029695	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35193529	0.94[EUR][1000 genomes]
rs35545963	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35567364	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35679974	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35692484	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35981245	0.88[AMR][1000 genomes]
rs3850967	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4338625	0.94[EUR][1000 genomes]
rs4930977	0.91[AMR][1000 genomes]
rs4930981	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4930983	0.94[EUR][1000 genomes]
rs4931485	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931498	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931510	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4931518	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55635343	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs55643034	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56183451	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56234529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56282720	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56327034	1.00[ASN][1000 genomes]
rs56409505	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs66479670	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66520413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66552209	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66597773	0.86[EUR][1000 genomes]
rs66635949	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67415228	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67963293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68030436	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455664	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71455667	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71455668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455670	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71455671	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73080503	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73084486	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73086471	0.94[EUR][1000 genomes]
rs73088505	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73088597	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31536400-31624600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:31542400-31645000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:31549800-31618000	Weak transcription	Pancreas	Pancrea
4	chr12:31557200-31623600	Weak transcription	Hela-S3	cervix
5	chr12:31562400-31620600	Weak transcription	Brain Angular Gyrus	brain
6	chr12:31562400-31644400	Weak transcription	Brain Substantia Nigra	brain
7	chr12:31567400-31635800	Weak transcription	Osteobl	bone
8	chr12:31567800-31642800	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:31572000-31612600	Weak transcription	HSMM	muscle
10	chr12:31572000-31631200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:31572000-31631200	Weak transcription	HSMMtube	muscle
12	chr12:31572400-31620200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:31572400-31627400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:31572400-31628400	Weak transcription	Right Ventricle	heart
15	chr12:31572400-31631200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:31577800-31649400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:31579000-31632000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:31579200-31611800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:31579400-31626400	Weak transcription	Left Ventricle	heart
20	chr12:31579400-31632000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:31579600-31612400	Weak transcription	Fetal Brain Female	brain
22	chr12:31583400-31662000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:31585000-31631600	Weak transcription	Brain Anterior Caudate	brain
24	chr12:31585000-31642000	Weak transcription	Fetal Kidney	kidney
25	chr12:31585200-31620200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:31585400-31631800	Weak transcription	Fetal Lung	lung
27	chr12:31586200-31635800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:31588000-31615400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:31592000-31615000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:31594400-31648400	Weak transcription	Small Intestine	intestine
31	chr12:31598000-31615000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:31598200-31615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:31598600-31618000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:31600200-31626400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:31600600-31619600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:31600600-31630400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:31600600-31632000	Weak transcription	Brain Germinal Matrix	brain
38	chr12:31600800-31631600	Weak transcription	Adipose Nuclei	Adipose
39	chr12:31603600-31619200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:31603800-31632600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:31604400-31614800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:31605200-31618000	Weak transcription	Aorta	Aorta
43	chr12:31605400-31611400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:31605400-31613000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:31605400-31618000	Weak transcription	Spleen	Spleen
46	chr12:31605400-31630800	Weak transcription	Fetal Muscle Leg	muscle
47	chr12:31605400-31631200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:31605400-31647200	Weak transcription	Psoas Muscle	Psoas
49	chr12:31605600-31612600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:31605600-31618800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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