Variant report

Variant	rs17886354
Chromosome Location	chr1:45269333-45269334
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45268926-45269611	GM12891	blood:	n/a	n/a
2	POLR2A	chr1:45269004-45269716	K562	blood:	n/a	n/a
3	POLR2A	chr1:45269000-45270038	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:45267436-45270498	HCT-116	colon:	n/a	n/a
5	POLR2A	chr1:45267875-45269815	K562	blood:	n/a	n/a
6	POLR2A	chr1:45268260-45270299	A549	lung:	n/a	n/a
7	POLR2A	chr1:45269040-45270010	Hela-S3	cervix:	n/a	n/a
8	TCF7L2	chr1:45269236-45269628	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:45267267-45270518	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:45268939-45270587	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:45267248-45270541	Hela-S3	cervix:	n/a	n/a
12	HEY1	chr1:45268760-45270383	K562	blood:	n/a	n/a
13	POLR2A	chr1:45268871-45270543	K562	blood:	n/a	n/a
14	POLR2A	chr1:45269180-45269764	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:45268907-45269333	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:45269168-45269969	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:45268850-45269914	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:45269272-45269347	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:45268884-45270109	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:45268782-45269572	K562	blood:	n/a	n/a
21	POLR2A	chr1:45268897-45269429	K562	blood:	n/a	n/a

No data

(count:6 , 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	chr1:45240022..45242639-chr1:45267540..45269350,2	MCF-7	breast:
5	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
6	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

No data

Variant related genes	Relation type
PLK3	TF binding region
BTBD19	TF binding region
ENSG00000142945	Chromatin interaction
ENSG00000234093	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000142959	Chromatin interaction
ENSG00000199377	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs72676543	0.86[AFR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17886354	C1orf84	cis	parietal	SCAN

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	chr1:45266800-45272600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:45267200-45269800	Transcr. at gene 5' and 3'	NHEK	skin
6	chr1:45267200-45270200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:45267200-45270400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
8	chr1:45267400-45272800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
9	chr1:45267600-45269400	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
10	chr1:45267600-45269600	Transcr. at gene 5' and 3'	HSMMtube	muscle
11	chr1:45267600-45269800	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr1:45267600-45269800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:45267600-45269800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:45267600-45269800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:45267600-45269800	Transcr. at gene 5' and 3'	HSMM	muscle
16	chr1:45267600-45270200	Transcr. at gene 5' and 3'	Esophagus	oesophagus
17	chr1:45267600-45270400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:45267600-45272800	Genic enhancers	Spleen	Spleen
19	chr1:45267800-45272000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:45268000-45269800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:45268000-45272400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:45268200-45269400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:45268200-45269600	Enhancers	Right Atrium	heart
24	chr1:45268200-45269800	Enhancers	Fetal Brain Male	brain
25	chr1:45268200-45269800	Genic enhancers	Left Ventricle	heart
26	chr1:45268200-45270000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:45268200-45270000	Strong transcription	Primary hematopoietic stem cells	blood
28	chr1:45268200-45271800	Weak transcription	Fetal Heart	heart
29	chr1:45268200-45271800	Weak transcription	Psoas Muscle	Psoas
30	chr1:45268200-45272200	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr1:45268200-45272200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:45268200-45272400	Genic enhancers	Pancreas	Pancrea
33	chr1:45268200-45272400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:45268200-45272400	Genic enhancers	Stomach Smooth Muscle	stomach
35	chr1:45268200-45272600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:45268200-45272600	Genic enhancers	Lung	lung
37	chr1:45268200-45274200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr1:45268400-45269400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr1:45268400-45269400	Genic enhancers	Brain Angular Gyrus	brain
40	chr1:45268400-45269800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:45268400-45269800	Genic enhancers	Duodenum Mucosa	Duodenum
42	chr1:45268400-45269800	Genic enhancers	Fetal Thymus	thymus
43	chr1:45268400-45270200	Genic enhancers	Brain Cingulate Gyrus	brain
44	chr1:45268400-45270400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr1:45268400-45270600	Strong transcription	Fetal Lung	lung
46	chr1:45268400-45271600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:45268400-45271800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:45268400-45271800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:45268400-45271800	Strong transcription	Aorta	Aorta
50	chr1:45268400-45271800	Strong transcription	Ovary	ovary

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