Variant report

Variant	rs34955459
Chromosome Location	chr12:31557622-31557623
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31555515..31557727-chr12:31742803..31745185,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170456	Chromatin interaction
ENSG00000255867	Chromatin interaction

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

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

rs_ID	r²[population]
rs12809140	0.84[EUR][1000 genomes]
rs12812075	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12812141	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816170	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816386	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12818749	0.90[EUR][1000 genomes]
rs12819062	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12820294	0.90[EUR][1000 genomes]
rs12821808	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822601	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825207	0.92[EUR][1000 genomes]
rs12826193	0.86[EUR][1000 genomes]
rs12831480	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17497517	0.90[EUR][1000 genomes]
rs17497656	0.90[EUR][1000 genomes]
rs17497998	0.90[EUR][1000 genomes]
rs1879399	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126897	0.90[EUR][1000 genomes]
rs34007930	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34094545	0.86[EUR][1000 genomes]
rs34184789	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34271764	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34308937	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34450466	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585237	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34642866	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34667511	0.84[EUR][1000 genomes]
rs34949976	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34986122	0.90[EUR][1000 genomes]
rs35029695	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35193529	0.90[EUR][1000 genomes]
rs35545963	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35567364	0.84[EUR][1000 genomes]
rs35679974	0.87[EUR][1000 genomes]
rs35692484	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35981245	0.81[AMR][1000 genomes]
rs3850967	0.84[EUR][1000 genomes]
rs4338625	0.90[EUR][1000 genomes]
rs4930977	0.84[AMR][1000 genomes]
rs4930981	0.90[EUR][1000 genomes]
rs4930983	0.90[EUR][1000 genomes]
rs4931485	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931498	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931503	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931504	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931510	0.90[EUR][1000 genomes]
rs4931518	0.90[EUR][1000 genomes]
rs55635343	0.87[EUR][1000 genomes]
rs55643034	0.89[EUR][1000 genomes]
rs55771933	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56183451	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56234529	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56282720	0.87[EUR][1000 genomes]
rs56327034	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56409505	0.90[EUR][1000 genomes]
rs66479670	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66520413	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66552209	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66597773	0.85[EUR][1000 genomes]
rs66635949	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67415228	0.90[EUR][1000 genomes]
rs67963293	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68030436	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455661	0.82[EUR][1000 genomes]
rs71455664	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71455667	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71455668	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455669	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71455670	0.89[EUR][1000 genomes]
rs71455671	0.90[EUR][1000 genomes]
rs73080503	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73084486	0.90[EUR][1000 genomes]
rs73086471	0.90[EUR][1000 genomes]
rs73088505	0.89[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:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31535600-31560600	Weak transcription	Osteobl	bone
2	chr12:31536400-31624600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:31536600-31577400	Weak transcription	Small Intestine	intestine
4	chr12:31537400-31604800	Weak transcription	Spleen	Spleen
5	chr12:31537600-31580800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:31537800-31572400	Weak transcription	Stomach Mucosa	stomach
7	chr12:31538600-31563400	Weak transcription	Colonic Mucosa	Colon
8	chr12:31539800-31584800	Weak transcription	Fetal Heart	heart
9	chr12:31540400-31565200	Weak transcription	HUVEC	blood vessel
10	chr12:31540800-31563400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:31540800-31565400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:31540800-31572200	Weak transcription	Lung	lung
13	chr12:31540800-31573200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:31540800-31576800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:31542000-31578400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:31542200-31566000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:31542200-31583600	Weak transcription	Placenta	Placenta
18	chr12:31542400-31564600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:31542400-31565400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:31542400-31571200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:31542400-31645000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:31542600-31605800	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:31542800-31575400	Weak transcription	Fetal Brain Male	brain
24	chr12:31542800-31578800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:31544200-31579000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:31544400-31581400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:31544600-31584200	Weak transcription	Fetal Lung	lung
28	chr12:31544800-31565000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:31544800-31576200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:31545400-31559200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:31545800-31560400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr12:31545800-31583600	Weak transcription	Psoas Muscle	Psoas
33	chr12:31548800-31566200	Weak transcription	Fetal Kidney	kidney
34	chr12:31549800-31561800	Weak transcription	Brain Angular Gyrus	brain
35	chr12:31549800-31618000	Weak transcription	Pancreas	Pancrea
36	chr12:31550800-31573200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:31551400-31561800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:31551600-31558000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr12:31551600-31564800	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:31551800-31559000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:31553000-31565000	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:31554800-31560400	Weak transcription	Left Ventricle	heart
43	chr12:31554800-31560600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:31554800-31560600	Weak transcription	Right Ventricle	heart
45	chr12:31555000-31560400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:31555000-31565400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr12:31555200-31560200	Weak transcription	Brain Germinal Matrix	brain
48	chr12:31555200-31560400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:31555200-31561600	Weak transcription	Fetal Brain Female	brain
50	chr12:31555200-31566200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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