Variant report

Variant	rs59895800
Chromosome Location	chr1:45250007-45250008
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:113)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:113 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:45249876-45250114	GM12892	blood:	n/a	n/a
2	MYC	chr1:45249606-45250370	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:45249663-45250196	HepG2	liver:	n/a	n/a
4	YY1	chr1:45249620-45250512	HepG2	liver:	n/a	chr1:45250192-45250203
5	MYC	chr1:45249877-45250381	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:45249782-45250651	HepG2	liver:	n/a	n/a
7	ZBTB7A	chr1:45249816-45250023	HepG2	liver:	n/a	n/a
8	EGR1	chr1:45249816-45250095	GM12878	blood:	n/a	chr1:45249952-45249966
9	RAD21	chr1:45249904-45250015	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:45249775-45250171	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:45249042-45250722	H1-hESC	embryonic stem cell:	n/a	n/a
12	YY1	chr1:45249599-45250157	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr1:45250000-45250150	AG04449	skin:	n/a	n/a
14	RUNX3	chr1:45249626-45250923	GM12878	blood:	n/a	n/a
15	CTCF	chr1:45249980-45250130	GM12875	blood:	n/a	n/a
16	POLR2A	chr1:45249615-45250173	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:45249311-45250859	GM12892	blood:	n/a	n/a
18	RCOR1	chr1:45249870-45250022	HepG2	liver:	n/a	n/a
19	POLR2A	chr1:45249668-45250198	GM19193	blood:	n/a	n/a
20	POLR2A	chr1:45239529-45250168	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr1:45249864-45250130	A549	lung:	n/a	n/a
22	ELF1	chr1:45249858-45250143	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:45249888-45250127	MCF-7	breast:	n/a	n/a
24	STAT5A	chr1:45249312-45250017	GM12878	blood:	n/a	n/a
25	MAX	chr1:45249580-45250723	HepG2	liver:	n/a	n/a
26	CTCF	chr1:45249860-45250010	GM12874	blood:	n/a	n/a
27	CTCF	chr1:45249844-45250084	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:45249732-45250136	HepG2	liver:	n/a	n/a
29	MAX	chr1:45249543-45250745	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:45249798-45250147	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr1:45249940-45250090	GM12866	blood:	n/a	n/a
32	MAX	chr1:45249658-45250327	GM12878	blood:	n/a	n/a
33	MYC	chr1:45249908-45250172	MCF-7	breast:	n/a	n/a
34	POLR2A	chr1:45249730-45250631	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr1:45249991-45250069	GM19240	blood:	n/a	n/a
36	CEBPD	chr1:45249770-45250157	HepG2	liver:	n/a	n/a
37	POLR2A	chr1:45249224-45250912	HepG2	liver:	n/a	n/a
38	POLR2A	chr1:45249807-45250052	A549	lung:	n/a	n/a
39	POLR2A	chr1:45249816-45250487	MCF-7	breast:	n/a	n/a
40	CTCF	chr1:45249941-45250111	GM19239	blood:	n/a	n/a
41	GABPA	chr1:45249761-45250127	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr1:45248408-45250153	NB4	blood:	n/a	n/a
43	CTCF	chr1:45249860-45250010	SK-N-SH_RA	brain:	n/a	n/a
44	MXI1	chr1:45249659-45250044	GM12878	blood:	n/a	n/a
45	MAX	chr1:45249736-45250507	H1-hESC	embryonic stem cell:	n/a	n/a
46	TAF1	chr1:45249758-45250424	HepG2	liver:	n/a	n/a
47	TAF1	chr1:45249764-45250159	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:45249395-45250127	GM12891	blood:	n/a	n/a
49	POLR2A	chr1:45249764-45250101	GM12878	blood:	n/a	n/a
50	ZBTB7A	chr1:45249782-45250202	HepG2	liver:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45246917..45250948-chr1:45965225..45967473,3	K562	blood:
2	chr1:45248852..45254229-chr1:45263166..45267959,10	MCF-7	breast:
3	chr1:45194298..45199848-chr1:45247467..45253056,11	MCF-7	breast:
4	chr1:45249665..45252249-chr1:45973205..45975884,2	K562	blood:
5	chr1:45248846..45251148-chr1:46047782..46051549,3	K562	blood:
6	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
7	chr1:45248546..45252735-chr1:45278815..45281288,3	MCF-7	breast:
8	chr1:45248577..45250762-chr1:45371713..45373726,2	K562	blood:
9	chr1:45246681..45259677-chr1:45281336..45290057,25	MCF-7	breast:
10	chr1:45248330..45252127-chr1:45262500..45268022,8	MCF-7	breast:
11	chr1:45249917..45251811-chr1:45804784..45807136,2	K562	blood:
12	chr1:45249649..45251361-chr1:45272791..45275653,2	MCF-7	breast:
13	chr1:45194501..45200206-chr1:45249194..45253143,8	MCF-7	breast:
14	chr1:45248400..45253844-chr1:45268438..45273783,8	MCF-7	breast:
15	chr1:45248466..45253060-chr1:45282997..45288611,7	MCF-7	breast:

No data

Variant related genes	Relation type
RPS15AP11	TF binding region
ENSG00000132763	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12057238	0.89[ASN][1000 genomes]
rs12057414	0.96[ASN][1000 genomes]
rs12402781	0.89[ASN][1000 genomes]
rs12404160	0.83[ASN][1000 genomes]
rs12407290	0.88[ASN][1000 genomes]
rs12407627	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17391430	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17883304	0.88[ASN][1000 genomes]
rs17885815	0.83[ASN][1000 genomes]
rs3795712	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3795715	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806398	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3923304	0.88[ASN][1000 genomes]
rs41269079	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4520451	0.83[ASN][1000 genomes]
rs4565758	0.88[ASN][1000 genomes]
rs55703843	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58532407	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58603818	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60452778	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60766209	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72674017	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72674023	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	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	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv947252	chr1:45242176-45258816	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45244600-45251600	Weak transcription	Small Intestine	intestine
2	chr1:45245000-45258600	Weak transcription	Hela-S3	cervix
3	chr1:45246400-45251400	Weak transcription	HSMMtube	muscle
4	chr1:45247200-45251200	Weak transcription	K562	blood
5	chr1:45247400-45251400	Weak transcription	A549	lung
6	chr1:45249200-45251600	Enhancers	Primary T cells from cord blood	blood
7	chr1:45249200-45252600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:45249400-45250200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
9	chr1:45249400-45250200	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:45249400-45250400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr1:45249400-45250400	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr1:45249400-45250600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:45249400-45250600	Active TSS	Brain Angular Gyrus	brain
14	chr1:45249400-45251000	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr1:45249400-45251200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:45249400-45251400	Enhancers	NH-A	brain
17	chr1:45249400-45251600	Enhancers	Liver	Liver
18	chr1:45249400-45251600	Enhancers	Stomach Mucosa	stomach
19	chr1:45249400-45251800	Enhancers	Placenta	Placenta
20	chr1:45249400-45252000	Enhancers	Spleen	Spleen
21	chr1:45249600-45250200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:45249600-45250200	Active TSS	Brain Cingulate Gyrus	brain
23	chr1:45249600-45250400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr1:45249600-45250400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:45249600-45250400	Flanking Active TSS	Fetal Thymus	thymus
26	chr1:45249600-45250400	Active TSS	HSMM	muscle
27	chr1:45249600-45250600	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr1:45249600-45250600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:45249600-45250600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:45249600-45250600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:45249600-45250600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr1:45249600-45250600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:45249600-45250600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:45249600-45250600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:45249600-45250600	Active TSS	Fetal Kidney	kidney
36	chr1:45249600-45250600	Flanking Active TSS	Fetal Muscle Trunk	muscle
37	chr1:45249600-45250600	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr1:45249600-45250600	Flanking Active TSS	HMEC	breast
39	chr1:45249600-45250800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr1:45249600-45250800	Flanking Active TSS	Colonic Mucosa	Colon
41	chr1:45249600-45251000	Enhancers	Fetal Brain Male	brain
42	chr1:45249800-45250200	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr1:45249800-45250200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr1:45249800-45250200	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr1:45249800-45250200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:45249800-45250200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:45249800-45250200	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr1:45249800-45250200	Active TSS	Primary B cells from peripheral blood	blood
49	chr1:45249800-45250200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr1:45249800-45250200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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