Variant report

Variant	rs12404160
Chromosome Location	chr1:45268382-45268383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45267156-45268769	K562	blood:	n/a	n/a
2	STAT5A	chr1:45267773-45268596	GM12878	blood:	n/a	chr1:45268411-45268423
3	POLR2A	chr1:45267436-45270498	HCT-116	colon:	n/a	n/a
4	POLR2A	chr1:45268350-45268781	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:45267438-45268565	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:45268138-45268852	K562	blood:	n/a	n/a
7	POLR2A	chr1:45268318-45268607	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:45267875-45269815	K562	blood:	n/a	n/a
9	POLR2A	chr1:45268260-45270299	A549	lung:	n/a	n/a
10	POLR2A	chr1:45267829-45268567	HL-60	blood:	n/a	n/a
11	POLR2A	chr1:45268303-45269289	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr1:45267267-45270518	Hela-S3	cervix:	n/a	n/a
13	HEY1	chr1:45268377-45268603	K562	blood:	n/a	n/a
14	POLR2A	chr1:45267670-45268578	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:45267677-45268775	HepG2	liver:	n/a	n/a
16	HEY1	chr1:45268342-45268613	K562	blood:	n/a	n/a
17	POLR2A	chr1:45267421-45268706	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr1:45267248-45270541	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:45267469-45268891	GM12878	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45186012..45189065-chr1:45262922..45268915,8	MCF-7	breast:
2	chr1:45194156..45199355-chr1:45264282..45268731,9	MCF-7	breast:
3	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
4	chr1:45240022..45242639-chr1:45267540..45269350,2	MCF-7	breast:
5	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
6	chr1:45210802..45212965-chr1:45265931..45268698,2	K562	blood:
7	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

No data

Variant related genes	Relation type
PLK3	TF binding region
ENSG00000207421	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000234093	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000142959	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000264294	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12057238	0.93[ASN][1000 genomes]
rs12057414	0.86[ASN][1000 genomes]
rs12402781	0.93[ASN][1000 genomes]
rs12404244	0.94[EUR][1000 genomes]
rs12405110	0.81[EUR][1000 genomes]
rs12407290	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12407627	0.85[ASN][1000 genomes]
rs12408763	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16832249	0.83[EUR][1000 genomes]
rs16832251	0.82[EUR][1000 genomes]
rs16832301	0.84[ASN][1000 genomes]
rs17390300	0.84[ASN][1000 genomes]
rs17391430	0.85[ASN][1000 genomes]
rs17392632	0.84[ASN][1000 genomes]
rs17883304	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17885815	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295996	0.82[EUR][1000 genomes]
rs263961	0.82[ASN][1000 genomes]
rs3795712	0.80[ASN][1000 genomes]
rs3795715	0.82[ASN][1000 genomes]
rs3795718	0.90[EUR][1000 genomes]
rs3806398	0.85[ASN][1000 genomes]
rs3923304	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4073112	0.98[EUR][1000 genomes]
rs41269079	0.85[ASN][1000 genomes]
rs41269085	0.82[EUR][1000 genomes]
rs4520451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4565758	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59552012	0.84[ASN][1000 genomes]
rs59803789	0.94[EUR][1000 genomes]
rs59895800	0.83[ASN][1000 genomes]
rs60189524	0.86[EUR][1000 genomes]
rs60452778	0.86[ASN][1000 genomes]
rs60741033	0.84[ASN][1000 genomes]
rs60787198	0.84[ASN][1000 genomes]
rs6657078	0.84[EUR][1000 genomes]
rs6678737	0.90[EUR][1000 genomes]
rs72674017	0.82[ASN][1000 genomes]
rs72674023	0.85[ASN][1000 genomes]
rs72674049	0.83[EUR][1000 genomes]
rs72674051	0.81[EUR][1000 genomes]
rs72674081	0.84[ASN][1000 genomes]
rs72674084	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
8	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases
11	nsv871320	chr1:45259295-45274841	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	58 gene(s)	inside rSNPs	diseases
12	nsv870773	chr1:45259295-45287306	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases
13	nsv870876	chr1:45264545-45273531	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	56 gene(s)	inside rSNPs	diseases
14	nsv546147	chr1:45264874-45271097	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	44 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	chr1:45265600-45276600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:45266200-45268400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr1:45266200-45270400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:45266400-45268400	Flanking Active TSS	Fetal Thymus	thymus
5	chr1:45266400-45268600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:45266600-45276400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:45266800-45268800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:45266800-45272600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:45267000-45268400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:45267200-45268400	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:45267200-45268600	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:45267200-45269800	Transcr. at gene 5' and 3'	NHEK	skin
13	chr1:45267200-45270200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:45267200-45270400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
15	chr1:45267400-45268400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:45267400-45268400	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
17	chr1:45267400-45268400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr1:45267400-45269200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:45267400-45272800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
20	chr1:45267600-45268400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:45267600-45268400	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr1:45267600-45268400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
23	chr1:45267600-45268400	Flanking Active TSS	Brain Angular Gyrus	brain
24	chr1:45267600-45268400	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr1:45267600-45268400	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
26	chr1:45267600-45268400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr1:45267600-45268400	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
28	chr1:45267600-45268400	Transcr. at gene 5' and 3'	Placenta	Placenta
29	chr1:45267600-45268400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
30	chr1:45267600-45268400	Weak transcription	Small Intestine	intestine
31	chr1:45267600-45268600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:45267600-45268600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr1:45267600-45268600	Genic enhancers	Liver	Liver
34	chr1:45267600-45268600	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr1:45267600-45268600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
36	chr1:45267600-45268600	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
37	chr1:45267600-45268600	Flanking Active TSS	HUVEC	blood vessel
38	chr1:45267600-45268600	Transcr. at gene 5' and 3'	Osteobl	bone
39	chr1:45267600-45268800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:45267600-45268800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:45267600-45268800	Transcr. at gene 5' and 3'	HMEC	breast
42	chr1:45267600-45268800	Transcr. at gene 5' and 3'	NHLF	lung
43	chr1:45267600-45269000	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr1:45267600-45269000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:45267600-45269000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:45267600-45269000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
47	chr1:45267600-45269200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
48	chr1:45267600-45269200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
49	chr1:45267600-45269400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
50	chr1:45267600-45269600	Transcr. at gene 5' and 3'	HSMMtube	muscle

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