Variant report

Variant	rs4520451
Chromosome Location	chr1:45270733-45270734
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45270630-45276680	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:45270664-45274484	K562	blood:	n/a	n/a
3	POLR2A	chr1:45270697-45276683	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:45270122-45271397	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:45270657-45276553	K562	blood:	n/a	n/a
6	POLR2A	chr1:45270691-45271518	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:45270671-45276445	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:45270669-45276523	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:45270667-45271363	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:45270691-45271557	K562	blood:	n/a	n/a
11	POLR2A	chr1:45270724-45271394	GM12891	blood:	n/a	n/a
12	POLR2A	chr1:45270711-45271873	HCT-116	colon:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45248400..45253844-chr1:45268438..45273783,8	MCF-7	breast:
2	chr1:45268954..45275189-chr1:45475024..45480055,7	K562	blood:
3	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
4	chr1:45194189..45198394-chr1:45270401..45277394,13	MCF-7	breast:
5	chr1:45269727..45273120-chr1:45475175..45479286,6	K562	blood:
6	chr1:45240969..45242475-chr1:45269379..45271647,2	MCF-7	breast:
7	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
8	chr1:45186115..45188704-chr1:45270219..45273209,3	MCF-7	breast:
9	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

No data

Variant related genes	Relation type
BTBD19	TF binding region
ENSG00000202031	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000142959	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000234093	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 59 )
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]
rs12404160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
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:16 , 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
15	esv3354434	chr1:45269765-45274063	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	35 gene(s)	inside rSNPs	diseases
16	esv3340963	chr1:45270390-45273238	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	31 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	chr1:45266600-45276400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:45266800-45272600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:45267400-45272800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
5	chr1:45267600-45272800	Genic enhancers	Spleen	Spleen
6	chr1:45267800-45272000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:45268000-45272400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:45268200-45271800	Weak transcription	Fetal Heart	heart
9	chr1:45268200-45271800	Weak transcription	Psoas Muscle	Psoas
10	chr1:45268200-45272200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr1:45268200-45272200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:45268200-45272400	Genic enhancers	Pancreas	Pancrea
13	chr1:45268200-45272400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
14	chr1:45268200-45272400	Genic enhancers	Stomach Smooth Muscle	stomach
15	chr1:45268200-45272600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:45268200-45272600	Genic enhancers	Lung	lung
17	chr1:45268200-45274200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:45268400-45271600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:45268400-45271800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:45268400-45271800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:45268400-45271800	Strong transcription	Aorta	Aorta
22	chr1:45268400-45271800	Strong transcription	Ovary	ovary
23	chr1:45268400-45271800	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:45268400-45271800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:45268400-45272400	Strong transcription	Fetal Stomach	stomach
26	chr1:45268400-45272600	Genic enhancers	Right Ventricle	heart
27	chr1:45268400-45272800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:45268400-45272800	Genic enhancers	Placenta	Placenta
29	chr1:45268400-45272800	Strong transcription	Dnd41	blood
30	chr1:45268400-45273200	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr1:45268600-45271000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:45268600-45271200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:45268600-45271200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr1:45268600-45271400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:45268600-45271600	Strong transcription	Liver	Liver
36	chr1:45268600-45271800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:45268600-45271800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:45268600-45272000	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr1:45268600-45272000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:45268600-45272200	Strong transcription	Fetal Intestine Large	intestine
41	chr1:45268600-45272200	Strong transcription	K562	blood
42	chr1:45268600-45272400	Strong transcription	Thymus	Thymus
43	chr1:45268600-45272400	Genic enhancers	HUVEC	blood vessel
44	chr1:45268600-45272400	Genic enhancers	NHDF-Ad	bronchial
45	chr1:45268600-45272800	Genic enhancers	Primary T cells from cord blood	blood
46	chr1:45268600-45272800	Genic enhancers	Fetal Muscle Trunk	muscle
47	chr1:45268600-45273200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:45268600-45273200	Genic enhancers	Fetal Muscle Leg	muscle
49	chr1:45268800-45271000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:45268800-45271000	Strong transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links