Variant report

Variant	rs17299030
Chromosome Location	chr8:125574613-125574614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:125573944-125575373	HepG2	liver:	n/a	n/a
2	CEBPB	chr8:125574554-125574841	K562	blood:	n/a	chr8:125574678-125574687 chr8:125574677-125574688 chr8:125574678-125574687 chr8:125574678-125574687 chr8:125574678-125574687
3	CEBPB	chr8:125574510-125574840	HepG2	liver:	n/a	chr8:125574678-125574687 chr8:125574677-125574688 chr8:125574678-125574687 chr8:125574678-125574687 chr8:125574678-125574687
4	CEBPB	chr8:125574600-125574814	IMR90	lung:	n/a	chr8:125574678-125574687 chr8:125574677-125574688 chr8:125574678-125574687 chr8:125574678-125574687 chr8:125574678-125574687
5	CEBPB	chr8:125574555-125574783	A549	lung:	n/a	chr8:125574678-125574687 chr8:125574677-125574688 chr8:125574678-125574687 chr8:125574678-125574687 chr8:125574678-125574687
6	CTCF	chr8:125574560-125574710	BE2_C	brain:	n/a	n/a
7	CEBPB	chr8:125574506-125574841	K562	blood:	n/a	chr8:125574678-125574687 chr8:125574677-125574688 chr8:125574678-125574687 chr8:125574678-125574687 chr8:125574678-125574687

No.	Distal block	Cell Line	Cell type
1	chr8:125560928..125566588-chr8:125566852..125577107,17	MCF-7	breast:
2	chr8:125572673..125575871-chr8:125577015..125582400,6	K562	blood:
3	chr8:125549460..125555106-chr8:125573452..125578755,9	MCF-7	breast:
4	chr8:125573757..125577202-chr8:125578987..125583404,3	MCF-7	breast:
5	chr8:125551424..125552952-chr8:125573257..125575450,2	K562	blood:
6	chr8:125569223..125571926-chr8:125574045..125576529,2	K562	blood:
7	chr8:125486165..125488789-chr8:125574025..125577553,3	MCF-7	breast:
8	chr8:125570314..125572061-chr8:125572775..125574818,2	MCF-7	breast:
9	chr8:125573683..125575467-chr8:125971520..125974069,2	MCF-7	breast:
10	chr8:125539308..125541314-chr8:125571807..125574800,2	MCF-7	breast:
11	chr8:125572972..125577628-chr8:125578200..125582090,6	MCF-7	breast:
12	chr8:125574370..125578079-chr8:125630160..125632086,3	MCF-7	breast:
13	chr8:125567601..125570100-chr8:125573465..125576752,3	MCF-7	breast:

Variant related genes	Relation type
MTSS1	TF binding region
ENSG00000170873	Chromatin interaction
ENSG00000147684	Chromatin interaction
ENSG00000245149	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000147687	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10505446	0.92[CEU][hapmap]
rs17298759	0.92[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17298884	0.92[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17298912	0.92[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299208	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299341	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17300503	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17372350	1.00[CEU][hapmap]
rs17372901	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4286935	0.86[CEU][hapmap]
rs4585740	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6470248	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7003602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7830235	0.92[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv465801	chr8:125565328-125576681	Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv612145	chr8:125565328-125576681	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv525649	chr8:125565328-125600818	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv465802	chr8:125570144-125576681	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv612146	chr8:125570144-125576681	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17299030	TRMT12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125553400-125575200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr8:125553400-125575200	Strong transcription	Fetal Muscle Leg	muscle
3	chr8:125553800-125575400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
5	chr8:125554200-125576200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:125554400-125575400	Strong transcription	Primary B cells from cord blood	blood
7	chr8:125554400-125576200	Strong transcription	Fetal Intestine Large	intestine
8	chr8:125554600-125575000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr8:125554600-125575800	Strong transcription	Stomach Smooth Muscle	stomach
10	chr8:125555200-125575000	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr8:125555200-125575200	Strong transcription	Brain Cingulate Gyrus	brain
12	chr8:125556200-125575000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr8:125556800-125576800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr8:125558000-125575600	Weak transcription	Stomach Mucosa	stomach
15	chr8:125560400-125575000	Weak transcription	Right Atrium	heart
16	chr8:125561200-125575200	Strong transcription	HepG2	liver
17	chr8:125561400-125575000	Strong transcription	Adipose Nuclei	Adipose
18	chr8:125561400-125575600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr8:125561600-125575000	Strong transcription	Liver	Liver
20	chr8:125563600-125575600	Strong transcription	Fetal Stomach	stomach
21	chr8:125564000-125575600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr8:125564400-125576800	Strong transcription	Fetal Intestine Small	intestine
23	chr8:125566000-125575000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr8:125566000-125576400	Weak transcription	GM12878-XiMat	blood
25	chr8:125566000-125602400	Weak transcription	Aorta	Aorta
26	chr8:125566200-125575800	Weak transcription	NHDF-Ad	bronchial
27	chr8:125566200-125590400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:125566400-125575000	Weak transcription	Dnd41	blood
29	chr8:125566400-125575800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr8:125566400-125575800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr8:125566400-125577600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr8:125566400-125577800	Weak transcription	Small Intestine	intestine
33	chr8:125566400-125600600	Weak transcription	NHEK	skin
34	chr8:125566600-125575200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr8:125566600-125576400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr8:125566600-125577200	Weak transcription	Osteobl	bone
37	chr8:125566800-125581400	Weak transcription	HSMM	muscle
38	chr8:125567000-125590200	Weak transcription	Fetal Brain Male	brain
39	chr8:125567200-125576200	Weak transcription	Fetal Heart	heart
40	chr8:125568000-125575000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr8:125568200-125575600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr8:125568200-125577000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr8:125568400-125575800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr8:125568600-125575000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr8:125568600-125576400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr8:125568800-125575600	Weak transcription	Ovary	ovary
47	chr8:125568800-125576400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr8:125569800-125575200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr8:125570000-125584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr8:125570400-125575200	Strong transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links