Variant report

Variant	rs12478564
Chromosome Location	chr2:233598340-233598341
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	NRF1	chr2:233598222-233598352	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000213055	TF binding region

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1022330	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1044480	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933409	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933411	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10933412	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11555646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676216	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11679079	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687128	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690474	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11692545	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12472839	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12474040	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694917	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12987513	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990821	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12991088	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997185	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13003675	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13003738	0.81[ASN][1000 genomes]
rs13004406	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13007783	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13008942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011298	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021246	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024793	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13035829	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13424351	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1446308	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446310	0.91[ASN][1000 genomes]
rs1446311	0.83[EUR][1000 genomes]
rs1801251	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867778	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1947105	0.81[EUR][1000 genomes]
rs2012221	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2044449	0.81[EUR][1000 genomes]
rs2100053	0.81[EUR][1000 genomes]
rs2305137	0.83[EUR][1000 genomes]
rs2305141	0.91[ASN][1000 genomes]
rs2592102	0.81[EUR][1000 genomes]
rs2592105	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592113	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2674839	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2675971	0.81[EUR][1000 genomes]
rs2675973	0.81[EUR][1000 genomes]
rs2675974	0.81[EUR][1000 genomes]
rs283466	0.91[ASN][1000 genomes]
rs283468	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs283469	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs283471	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs283474	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283475	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283476	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs283477	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs283478	0.82[ASN][1000 genomes]
rs283479	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283480	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283481	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283484	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283485	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283486	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33980184	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34880628	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35085837	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35212961	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35285732	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35362030	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35395584	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35621474	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36007169	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816334	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3817311	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452130	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4458205	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4517962	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4973053	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4973054	0.83[EUR][1000 genomes]
rs4973559	0.81[ASN][1000 genomes]
rs4973560	0.88[ASN][1000 genomes]
rs4973561	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs56777991	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437074	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66549961	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67013068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714245	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717841	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719061	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6724117	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732136	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733151	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738386	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739638	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6745879	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746294	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6747645	0.98[EUR][1000 genomes]
rs6748027	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761324	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71421663	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737028	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7558609	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7562712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7573208	0.89[ASN][1000 genomes]
rs7578299	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7587309	0.83[EUR][1000 genomes]
rs7589201	0.81[EUR][1000 genomes]
rs7591176	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7592717	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606090	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778166	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs895430	0.81[EUR][1000 genomes]
rs9653383	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9679089	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs983430	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs991873	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
3	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
4	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
5	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
7	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:233569200-233615000	Weak transcription	Colonic Mucosa	Colon
9	chr2:233569400-233612800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:233569400-233615400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:233571200-233627400	Weak transcription	Gastric	stomach
12	chr2:233571400-233601800	Weak transcription	Esophagus	oesophagus
13	chr2:233571600-233612200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:233580000-233606000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:233580600-233604000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:233585200-233655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:233585800-233604400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:233585800-233626000	Weak transcription	Fetal Heart	heart
19	chr2:233586400-233603200	Strong transcription	Fetal Thymus	thymus
20	chr2:233586400-233612200	Weak transcription	Brain Substantia Nigra	brain
21	chr2:233586800-233599000	Weak transcription	K562	blood
22	chr2:233587000-233630600	Weak transcription	Psoas Muscle	Psoas
23	chr2:233587200-233604400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:233587200-233613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:233588400-233599600	Strong transcription	Primary T cells from cord blood	blood
26	chr2:233588800-233605000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:233589000-233603600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:233589000-233605800	Strong transcription	Liver	Liver
29	chr2:233589600-233619800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:233589600-233627000	Weak transcription	Pancreas	Pancrea
31	chr2:233590400-233599200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:233590400-233601600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:233590600-233599200	Weak transcription	NH-A	brain
34	chr2:233590600-233599400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:233590600-233599400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr2:233590800-233601600	Weak transcription	Hela-S3	cervix
37	chr2:233591800-233602600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:233592200-233601600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:233592200-233604600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:233592600-233601200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:233592800-233603000	Strong transcription	Dnd41	blood
42	chr2:233593200-233601400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:233593800-233599000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:233594800-233599000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:233594800-233599000	Weak transcription	Brain Angular Gyrus	brain
46	chr2:233594800-233599400	Weak transcription	HSMM	muscle
47	chr2:233594800-233599600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:233594800-233611800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr2:233594800-233612400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:233595000-233598800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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