Variant report

Variant	rs2292559
Chromosome Location	chr1:226034774-226034775
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:226033237-226034940	K562	blood:	n/a	n/a
2	POLR2A	chr1:226029774-226034830	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr1:226029273-226035960	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:226034576-226034976	A549	lung:	n/a	n/a
5	POLR2A	chr1:226029747-226034951	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:226034596-226034954	K562	blood:	n/a	n/a
7	POLR2A	chr1:226033115-226034926	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr1:226034708-226034981	A549	lung:	n/a	n/a
9	POLR2A	chr1:226029446-226038446	K562	blood:	n/a	n/a
10	POLR2A	chr1:226034709-226034937	A549	lung:	n/a	n/a
11	POLR2A	chr1:226034623-226034959	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:226033177-226034919	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:226033065-226034778	K562	blood:	n/a	n/a
14	POLR2A	chr1:226030670-226038260	A549	lung:	n/a	n/a
15	POLR2A	chr1:226034735-226034977	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr1:226034680-226034947	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:226032510..226034899-chr1:226069383..226071490,2	MCF-7	breast:
2	chr1:226034669..226036597-chr1:226045740..226048084,2	K562	blood:
3	chr1:226033230..226036408-chr1:226061975..226066194,3	MCF-7	breast:
4	chr1:225963673..225968224-chr1:226032543..226034938,4	MCF-7	breast:
5	chr1:225964257..225969087-chr1:226030786..226035881,7	K562	blood:
6	chr1:225963873..225967033-chr1:226031330..226035962,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000242861	TF binding region
ENSG00000143742	Chromatin interaction
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10047091	0.90[EUR][1000 genomes]
rs12061043	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12071072	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12071104	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12074209	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12074247	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12075664	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236143	0.87[EUR][1000 genomes]
rs2271544	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292556	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292560	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292561	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292568	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28384446	0.92[EUR][1000 genomes]
rs28384447	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28384448	0.95[EUR][1000 genomes]
rs28384449	0.95[EUR][1000 genomes]
rs360084	0.99[ASN][1000 genomes]
rs360087	0.99[ASN][1000 genomes]
rs360089	0.99[ASN][1000 genomes]
rs3738050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738051	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753663	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753666	0.92[EUR][1000 genomes]
rs3753668	0.90[EUR][1000 genomes]
rs3753670	0.90[EUR][1000 genomes]
rs3766935	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766936	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766937	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766940	0.95[EUR][1000 genomes]
rs3766941	0.90[EUR][1000 genomes]
rs3806257	0.90[EUR][1000 genomes]
rs3806258	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41310561	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4149227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149228	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4149230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45467394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56231004	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56301120	1.00[ASN][1000 genomes]
rs56325807	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57095220	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57932384	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59728172	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60847271	0.95[EUR][1000 genomes]
rs60943392	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61033712	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61227102	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61295362	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6664740	0.90[EUR][1000 genomes]
rs74150536	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7514448	0.90[EUR][1000 genomes]
rs7516538	0.90[EUR][1000 genomes]
rs805179	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv1801609	chr1:226027323-226036309	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv1802694	chr1:226032229-226036309	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr1:226013600-226052600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:226013800-226037200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:226014600-226035600	Weak transcription	Small Intestine	intestine
4	chr1:226014800-226047800	Weak transcription	Psoas Muscle	Psoas
5	chr1:226016000-226051000	Weak transcription	NH-A	brain
6	chr1:226017400-226049800	Weak transcription	HUVEC	blood vessel
7	chr1:226020600-226042000	Weak transcription	Hela-S3	cervix
8	chr1:226020600-226042400	Weak transcription	HSMM	muscle
9	chr1:226023000-226039600	Weak transcription	NHDF-Ad	bronchial
10	chr1:226023800-226035800	Weak transcription	Fetal Brain Male	brain
11	chr1:226025800-226034800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:226025800-226036400	Strong transcription	Lung	lung
13	chr1:226025800-226036400	Strong transcription	Osteobl	bone
14	chr1:226026200-226035200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr1:226026800-226061600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:226029600-226035600	Genic enhancers	Brain Hippocampus Middle	brain
17	chr1:226029800-226035000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:226029800-226035200	Strong transcription	Fetal Brain Female	brain
19	chr1:226029800-226035400	Strong transcription	Spleen	Spleen
20	chr1:226029800-226037600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:226029800-226050600	Strong transcription	Right Ventricle	heart
22	chr1:226030000-226040200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:226030200-226039000	Genic enhancers	Brain Substantia Nigra	brain
24	chr1:226030400-226034800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:226030400-226036000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:226030400-226046800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:226030400-226052600	Weak transcription	HSMMtube	muscle
28	chr1:226030600-226039400	Strong transcription	Liver	Liver
29	chr1:226030800-226037000	Weak transcription	Right Atrium	heart
30	chr1:226030800-226037400	Strong transcription	NHLF	lung
31	chr1:226031200-226037200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:226031400-226037800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:226031800-226036600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:226031800-226039600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:226032000-226034800	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr1:226032000-226034800	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr1:226032000-226036200	Genic enhancers	Brain Angular Gyrus	brain
38	chr1:226032000-226037400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:226032000-226037800	Strong transcription	Aorta	Aorta
40	chr1:226032200-226036800	Strong transcription	Brain Germinal Matrix	brain
41	chr1:226032400-226036600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:226032400-226039000	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr1:226032600-226035400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:226033200-226034800	Genic enhancers	Placenta	Placenta
45	chr1:226033200-226035800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:226033200-226036000	Genic enhancers	Fetal Thymus	thymus
47	chr1:226033200-226036200	Genic enhancers	Brain Inferior Temporal Lobe	brain
48	chr1:226033200-226036600	Genic enhancers	Pancreas	Pancrea
49	chr1:226033200-226037200	Genic enhancers	Brain Anterior Caudate	brain
50	chr1:226033200-226039800	Genic enhancers	Brain Cingulate Gyrus	brain

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