Variant report

Variant	rs6489242
Chromosome Location	chr12:122613278-122613279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:122613216-122613447	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122515765..122517447-chr12:122610871..122613524,2	MCF-7	breast:
2	chr12:122612652..122615876-chr12:122685490..122688136,3	K562	blood:
3	chr12:122457603..122461416-chr12:122608714..122613817,5	MCF-7	breast:
4	chr12:122516422..122518612-chr12:122611562..122613358,2	MCF-7	breast:
5	chr12:122611551..122613611-chr12:122618331..122620182,2	K562	blood:
6	chr12:122611022..122613336-chr12:122620039..122621726,2	MCF-7	breast:

No data

Variant related genes	Relation type
MLXIP	TF binding region
ENSG00000176383	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000255856	Chromatin interaction
ENSG00000110987	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];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1047813	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10744177	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10744335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10773037	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10846525	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11057184	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11057654	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11057905	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11059094	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11060477	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11061156	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11061602	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11608788	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11608792	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11609875	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12366611	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28385906	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28401575	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28410367	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28414202	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28421373	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28430881	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28450064	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28453771	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28461580	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28464252	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28478366	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28478717	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28498002	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28498376	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28503672	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28506952	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28517281	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28529535	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28530689	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28545660	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28548845	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28569273	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28580546	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28585613	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28591322	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28605425	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28607028	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28613772	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28626850	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28631172	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28639626	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28642975	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28649184	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28652632	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28683032	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28699616	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28737311	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28739522	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34047484	0.86[EUR][1000 genomes]
rs34123446	0.87[EUR][1000 genomes]
rs34439774	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34532891	0.85[EUR][1000 genomes]
rs34741056	0.84[EUR][1000 genomes]
rs34974633	0.85[EUR][1000 genomes]
rs35249105	0.86[EUR][1000 genomes]
rs35676267	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35764187	0.85[EUR][1000 genomes]
rs36079122	0.81[EUR][1000 genomes]
rs3809117	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3892367	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758653	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4758654	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4758685	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4758686	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4758687	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4758688	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4758690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61952902	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61952904	0.85[EUR][1000 genomes]
rs61952920	0.82[EUR][1000 genomes]
rs61952922	0.88[EUR][1000 genomes]
rs61952923	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6489238	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6489244	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7312210	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73217796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7484733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7485054	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7485380	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7485447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487292	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7487608	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7488268	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7488393	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488857	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7953704	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7955571	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7955575	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7962500	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7964148	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7967127	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975001	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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:126 , 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	chr12:122599000-122614400	Weak transcription	Fetal Kidney	kidney
3	chr12:122608200-122618800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:122608200-122618800	Weak transcription	GM12878-XiMat	blood
5	chr12:122608400-122625400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:122608600-122613400	Weak transcription	NHDF-Ad	bronchial
7	chr12:122608600-122614200	Weak transcription	NH-A	brain
8	chr12:122608600-122632800	Strong transcription	Fetal Stomach	stomach
9	chr12:122610000-122614400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:122610000-122614400	Strong transcription	NHEK	skin
11	chr12:122610000-122615400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:122610000-122617400	Strong transcription	Primary B cells from cord blood	blood
13	chr12:122610000-122621800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:122610200-122619600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr12:122610200-122629200	Strong transcription	Primary T cells from cord blood	blood
16	chr12:122610200-122629200	Strong transcription	Fetal Thymus	thymus
17	chr12:122610400-122630600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:122610400-122630600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:122610600-122629200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:122610600-122629400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:122610600-122633200	Weak transcription	Right Atrium	heart
22	chr12:122610800-122628800	Strong transcription	Primary B cells from peripheral blood	blood
23	chr12:122610800-122630600	Strong transcription	Thymus	Thymus
24	chr12:122611000-122616200	Strong transcription	K562	blood
25	chr12:122611200-122613800	Weak transcription	Psoas Muscle	Psoas
26	chr12:122611200-122614200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr12:122611200-122616000	Strong transcription	Primary hematopoietic stem cells	blood
28	chr12:122611200-122620600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr12:122611200-122620800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:122611200-122626000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:122611200-122630400	Strong transcription	Gastric	stomach
32	chr12:122611400-122614600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:122611400-122615000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:122611400-122618600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:122611400-122628800	Strong transcription	Pancreas	Pancrea
36	chr12:122611400-122629800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr12:122611400-122630400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:122611600-122613800	Enhancers	Fetal Heart	heart
39	chr12:122611600-122614200	Strong transcription	Fetal Muscle Leg	muscle
40	chr12:122611600-122621200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:122611600-122629000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr12:122611600-122630000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:122611600-122630600	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:122611800-122613400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:122611800-122614000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:122611800-122614200	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr12:122611800-122614400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr12:122611800-122614600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:122611800-122614600	Strong transcription	Lung	lung
50	chr12:122611800-122615200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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