Variant report

Variant	rs12066809
Chromosome Location	chr1:45989428-45989429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr1:45989026-45989583	K562	blood:	n/a	n/a
2	CEBPD	chr1:45989124-45989687	K562	blood:	n/a	n/a
3	RCOR1	chr1:45989224-45989561	K562	blood:	n/a	n/a
4	GATA2	chr1:45989066-45989596	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
2	chr1:45975860..45989626-chr1:46030076..46041078,36	K562	blood:
3	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
4	chr1:45805140..45807328-chr1:45987853..45992059,3	K562	blood:
5	chr1:45985569..45992282-chr1:46014173..46025125,38	MCF-7	breast:
6	chr1:45982844..45990993-chr1:46030121..46038313,25	K562	blood:
7	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
8	chr1:45284051..45285694-chr1:45989373..45992080,2	K562	blood:
9	chr1:45284090..45287076-chr1:45986937..45989870,4	K562	blood:
10	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
11	chr1:45826987..45828662-chr1:45989193..45991039,2	K562	blood:

No data

Variant related genes	Relation type
PRDX1	TF binding region
ENSG00000132773	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000117448	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11211125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211127	1.00[EUR][1000 genomes]
rs12065695	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067882	1.00[EUR][1000 genomes]
rs12070890	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073047	1.00[EUR][1000 genomes]
rs12083690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091335	1.00[EUR][1000 genomes]
rs12093444	1.00[EUR][1000 genomes]
rs12565230	1.00[EUR][1000 genomes]
rs16832540	1.00[EUR][1000 genomes]
rs16832545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16832550	1.00[EUR][1000 genomes]
rs16832557	1.00[EUR][1000 genomes]
rs16832559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532613	1.00[EUR][1000 genomes]
rs28674795	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2934860	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934861	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934863	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934864	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991965	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2991967	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991969	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991984	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993256	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993260	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993261	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014222	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014223	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35067820	1.00[EUR][1000 genomes]
rs35103566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36053912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57910611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59050426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60347972	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60660559	1.00[EUR][1000 genomes]
rs6664588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72478602	1.00[ASN][1000 genomes]
rs72896187	1.00[EUR][1000 genomes]
rs72898313	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898323	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7412911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550744	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429080	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429083	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429164	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429165	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh 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	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
9	esv3522720	chr1:45989173-45989598	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
10	esv3363475	chr1:45989174-45989617	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	esv3522721	chr1:45989241-45989554	Weak transcription Enhancers	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45988200-45990000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr1:45988200-45990000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:45988200-45990600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:45988200-45990600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:45988200-45990800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:45988200-45990800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:45988200-45991000	Enhancers	Dnd41	blood
8	chr1:45988200-45992200	Weak transcription	Fetal Lung	lung
9	chr1:45988200-45993000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:45988400-45990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:45988400-45992200	Weak transcription	Fetal Intestine Large	intestine
12	chr1:45988400-45992200	Weak transcription	Fetal Kidney	kidney
13	chr1:45988400-45993400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:45988400-45997200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr1:45988600-45990000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:45988600-45990600	Weak transcription	HSMMtube	muscle
17	chr1:45988600-45991000	Weak transcription	Liver	Liver
18	chr1:45988600-45992200	Weak transcription	Fetal Heart	heart
19	chr1:45988600-45992200	Weak transcription	Fetal Intestine Small	intestine
20	chr1:45988600-45993400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:45988800-45989600	Enhancers	K562	blood
22	chr1:45988800-45989800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:45988800-45990600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:45988800-45990600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:45989000-45990600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr1:45989000-45990600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:45989000-45990600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:45989000-45990600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:45989000-45990600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:45989000-45990600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:45989000-45990600	Weak transcription	Stomach Mucosa	stomach
32	chr1:45989000-45993200	Weak transcription	Placenta	Placenta
33	chr1:45989200-45990200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:45989200-45990600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:45989200-45990600	Weak transcription	A549	lung
36	chr1:45989200-45990600	Weak transcription	HepG2	liver
37	chr1:45989200-46000600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:45989400-45990400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:45989400-45990400	Weak transcription	Hela-S3	cervix

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