Variant report

Variant	rs4758687
Chromosome Location	chr12:122616286-122616287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr12:122614200-122616643	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122237535..122239175-chr12:122615954..122617703,2	MCF-7	breast:
2	chr12:122353848..122356586-chr12:122614343..122616936,2	MCF-7	breast:

Variant related genes	Relation type
MLXIP	TF binding region
ENSG00000212694	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1047796	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1047813	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10744177	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10744335	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10773037	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10846525	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11057184	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11057654	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11057905	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11059094	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11060477	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11061156	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11061602	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608788	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11608792	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11609875	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12366611	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28385906	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28401575	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28410367	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28414202	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28421373	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28430881	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28450064	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28453771	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28461580	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28464252	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28478366	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28478717	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28498002	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28498376	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28503672	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28506952	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28517281	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28529535	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28530689	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28545660	0.80[EUR][1000 genomes]
rs28548845	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28569273	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28580546	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28585613	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28591322	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28605425	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28607028	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28613772	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28626850	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28631172	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28639626	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28642975	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28649184	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28652632	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28683032	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28699616	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28737311	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28739522	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34047484	0.83[EUR][1000 genomes]
rs34123446	0.85[EUR][1000 genomes]
rs34439774	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34532891	0.82[EUR][1000 genomes]
rs34741056	0.82[EUR][1000 genomes]
rs34974633	0.82[EUR][1000 genomes]
rs35249105	0.83[EUR][1000 genomes]
rs35676267	0.86[EUR][1000 genomes]
rs35764187	0.82[EUR][1000 genomes]
rs3809117	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3892367	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4758653	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4758654	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4758685	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4758686	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4758688	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4758690	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4758691	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61952902	0.82[EUR][1000 genomes]
rs61952904	0.83[EUR][1000 genomes]
rs61952920	0.81[EUR][1000 genomes]
rs61952922	0.86[EUR][1000 genomes]
rs61952923	0.85[EUR][1000 genomes]
rs6489238	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6489242	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6489244	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs709284	0.80[ASN][1000 genomes]
rs7312210	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73217796	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7484733	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7485054	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7485380	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7485447	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7486198	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7487292	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7487608	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7488268	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488393	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7488857	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7953704	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7955571	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7955575	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7962500	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964148	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7967127	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7975001	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122584200-122622000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:122608200-122618800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:122608200-122618800	Weak transcription	GM12878-XiMat	blood
4	chr12:122608400-122625400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:122608600-122632800	Strong transcription	Fetal Stomach	stomach
6	chr12:122610000-122617400	Strong transcription	Primary B cells from cord blood	blood
7	chr12:122610000-122621800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:122610200-122619600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:122610200-122629200	Strong transcription	Primary T cells from cord blood	blood
10	chr12:122610200-122629200	Strong transcription	Fetal Thymus	thymus
11	chr12:122610400-122630600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:122610400-122630600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:122610600-122629200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:122610600-122629400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:122610600-122633200	Weak transcription	Right Atrium	heart
16	chr12:122610800-122628800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr12:122610800-122630600	Strong transcription	Thymus	Thymus
18	chr12:122611200-122620600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:122611200-122620800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:122611200-122626000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:122611200-122630400	Strong transcription	Gastric	stomach
22	chr12:122611400-122618600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:122611400-122628800	Strong transcription	Pancreas	Pancrea
24	chr12:122611400-122629800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr12:122611400-122630400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr12:122611600-122621200	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:122611600-122629000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr12:122611600-122630000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:122611600-122630600	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:122611800-122616400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:122611800-122620800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:122611800-122620800	Strong transcription	Brain Germinal Matrix	brain
33	chr12:122611800-122621000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:122611800-122622000	Strong transcription	Placenta	Placenta
35	chr12:122611800-122624200	Strong transcription	Fetal Intestine Large	intestine
36	chr12:122611800-122624200	Strong transcription	Dnd41	blood
37	chr12:122611800-122624400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:122611800-122626400	Strong transcription	Spleen	Spleen
39	chr12:122611800-122628800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:122611800-122628800	Strong transcription	Fetal Lung	lung
41	chr12:122611800-122628800	Strong transcription	Rectal Smooth Muscle	rectum
42	chr12:122611800-122629000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr12:122611800-122629400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:122612000-122617600	Strong transcription	Ovary	ovary
45	chr12:122612000-122617800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr12:122612000-122620800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:122612000-122620800	Strong transcription	Brain Anterior Caudate	brain
48	chr12:122612000-122621000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr12:122612000-122622200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:122612000-122622400	Strong transcription	Brain Hippocampus Middle	brain

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