Variant report

Variant	rs17880471
Chromosome Location	chr1:45268724-45268725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 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	POLR2A	chr1:45268656-45268751	MCF-7	breast:	n/a	n/a
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	chr1:45268138-45268852	K562	blood:	n/a	n/a
6	GABPA	chr1:45268393-45268943	K562	blood:	n/a	n/a
7	POLR2A	chr1:45267875-45269815	K562	blood:	n/a	n/a
8	POLR2A	chr1:45268260-45270299	A549	lung:	n/a	n/a
9	POLR2A	chr1:45268303-45269289	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr1:45267267-45270518	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:45267677-45268775	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:45268487-45268764	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:45267248-45270541	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:45267469-45268891	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:45268398-45269223	GM12892	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	chr1:45248400..45253844-chr1:45268438..45273783,8	MCF-7	breast:
3	chr1:45194156..45199355-chr1:45264282..45268731,9	MCF-7	breast:
4	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
5	chr1:45240022..45242639-chr1:45267540..45269350,2	MCF-7	breast:
6	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
7	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

No data

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

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs16832247	1.00[YRI][hapmap]
rs17884653	1.00[YRI][hapmap]

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	chr1:45266200-45270400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:45266600-45276400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:45266800-45268800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:45266800-45272600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:45267200-45269800	Transcr. at gene 5' and 3'	NHEK	skin
7	chr1:45267200-45270200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:45267200-45270400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
9	chr1:45267400-45269200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:45267400-45272800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
11	chr1:45267600-45268800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:45267600-45268800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:45267600-45268800	Transcr. at gene 5' and 3'	HMEC	breast
14	chr1:45267600-45268800	Transcr. at gene 5' and 3'	NHLF	lung
15	chr1:45267600-45269000	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr1:45267600-45269000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:45267600-45269000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:45267600-45269000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
19	chr1:45267600-45269200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
20	chr1:45267600-45269200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
21	chr1:45267600-45269400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
22	chr1:45267600-45269600	Transcr. at gene 5' and 3'	HSMMtube	muscle
23	chr1:45267600-45269800	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr1:45267600-45269800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:45267600-45269800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:45267600-45269800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:45267600-45269800	Transcr. at gene 5' and 3'	HSMM	muscle
28	chr1:45267600-45270200	Transcr. at gene 5' and 3'	Esophagus	oesophagus
29	chr1:45267600-45270400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:45267600-45272800	Genic enhancers	Spleen	Spleen
31	chr1:45267800-45268800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:45267800-45268800	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:45267800-45268800	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
34	chr1:45267800-45268800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
35	chr1:45267800-45268800	Transcr. at gene 5' and 3'	Hela-S3	cervix
36	chr1:45267800-45269000	Enhancers	Stomach Mucosa	stomach
37	chr1:45267800-45269200	Transcr. at gene 5' and 3'	NH-A	brain
38	chr1:45267800-45272000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:45268000-45268800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:45268000-45269000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
41	chr1:45268000-45269200	Genic enhancers	Gastric	stomach
42	chr1:45268000-45269800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:45268000-45272400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:45268200-45268800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:45268200-45268800	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
46	chr1:45268200-45268800	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
47	chr1:45268200-45268800	Genic enhancers	Colonic Mucosa	Colon
48	chr1:45268200-45268800	Genic enhancers	Fetal Intestine Small	intestine
49	chr1:45268200-45269000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:45268200-45269000	Weak transcription	Rectal Mucosa Donor 29	rectum

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