Variant report

Variant	rs28585613
Chromosome Location	chr12:122598060-122598061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122514781..122518776-chr12:122593485..122598871,7	MCF-7	breast:
2	chr12:122597480..122599140-chr12:122601411..122603902,2	K562	blood:
3	chr12:122515231..122521385-chr12:122592674..122599384,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175727	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1047796	0.85[EUR][1000 genomes]
rs1047813	0.87[EUR][1000 genomes]
rs10744177	0.87[EUR][1000 genomes]
rs10744335	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10770189	0.80[EUR][1000 genomes]
rs10773037	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10846525	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11057184	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057654	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11057905	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11059094	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11060477	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061156	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11061602	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11608788	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11608792	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11609875	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11835818	0.83[EUR][1000 genomes]
rs12366611	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1976859	0.82[EUR][1000 genomes]
rs2280573	0.82[EUR][1000 genomes]
rs2280574	0.82[EUR][1000 genomes]
rs28385906	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28401575	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28410367	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28414202	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28421373	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28430881	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28450064	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28453771	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28461580	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28464252	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28478366	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28478717	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28498002	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28498376	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28503672	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28506952	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28517281	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28529535	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28530689	0.90[EUR][1000 genomes]
rs28545660	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28548845	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28569273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28580546	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28591322	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28605425	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28607028	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28613772	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28626850	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28629903	0.85[EUR][1000 genomes]
rs28631172	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28639626	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28642975	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28649184	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28652632	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28683032	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28691281	0.82[EUR][1000 genomes]
rs28699616	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28737311	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28739522	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28759327	0.82[EUR][1000 genomes]
rs34047484	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34123446	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34439774	0.84[EUR][1000 genomes]
rs34532891	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34741056	0.91[EUR][1000 genomes]
rs34974633	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35159488	0.80[EUR][1000 genomes]
rs35249105	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35676267	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35764187	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36079122	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3809117	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3892367	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4758653	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4758654	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4758685	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4758686	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4758687	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4758688	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4758690	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4758691	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56072019	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61952902	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61952904	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61952920	0.89[EUR][1000 genomes]
rs61952922	0.94[EUR][1000 genomes]
rs61952923	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6489238	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6489242	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6489244	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7137049	0.82[EUR][1000 genomes]
rs7312210	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73217796	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7484733	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7485054	0.85[EUR][1000 genomes]
rs7485380	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7485447	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7486198	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7487292	0.80[ASN][1000 genomes]
rs7487608	0.84[ASN][1000 genomes]
rs7488268	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7488393	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7488857	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7953704	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7955571	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7955575	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7962500	0.87[EUR][1000 genomes]
rs7964148	0.86[EUR][1000 genomes]
rs7967127	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7975001	0.87[EUR][1000 genomes];0.80[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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899569	chr12:122478728-122630909	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122583200-122612200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:122583800-122607600	Weak transcription	Fetal Brain Female	brain
3	chr12:122584200-122622000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:122584800-122601200	Weak transcription	Dnd41	blood
5	chr12:122585400-122601400	Weak transcription	Brain Germinal Matrix	brain
6	chr12:122587400-122598600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:122591000-122601800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr12:122591000-122606000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:122591200-122600600	Weak transcription	Thymus	Thymus
10	chr12:122591200-122601400	Weak transcription	Primary B cells from cord blood	blood
11	chr12:122591200-122601400	Weak transcription	Esophagus	oesophagus
12	chr12:122591200-122602800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:122592000-122601200	Weak transcription	Fetal Lung	lung
14	chr12:122592200-122598200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:122592200-122601000	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:122592200-122611800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:122592400-122599000	Weak transcription	Right Atrium	heart
18	chr12:122592400-122600600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:122592400-122600600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:122592400-122601000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:122592400-122601000	Weak transcription	Brain Angular Gyrus	brain
22	chr12:122592400-122601000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:122592400-122601200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:122592600-122600600	Weak transcription	Gastric	stomach
25	chr12:122592600-122601000	Weak transcription	Right Ventricle	heart
26	chr12:122592800-122601200	Weak transcription	Lung	lung
27	chr12:122592800-122601600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr12:122593200-122601200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:122593200-122601200	Weak transcription	Ovary	ovary
30	chr12:122593400-122598200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:122593400-122598800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:122593400-122598800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:122593400-122598800	Weak transcription	HepG2	liver
34	chr12:122593400-122598800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr12:122593400-122601200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:122593400-122601200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:122593400-122607600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:122593600-122601600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr12:122593600-122606200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr12:122593600-122606200	Weak transcription	HUVEC	blood vessel
41	chr12:122593600-122607600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:122593600-122607600	Weak transcription	NHLF	lung
43	chr12:122594000-122598600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:122594200-122601600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:122594400-122598800	Weak transcription	Small Intestine	intestine
46	chr12:122594400-122599000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr12:122594400-122601000	Weak transcription	Fetal Muscle Leg	muscle
48	chr12:122594400-122601600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:122594600-122600400	Weak transcription	Adipose Nuclei	Adipose
50	chr12:122594600-122601200	Weak transcription	Psoas Muscle	Psoas

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