Variant report

Variant	rs17299208
Chromosome Location	chr8:125576681-125576682
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	CTCF	chr8:125576620-125576770	HUVEC	blood vessel:	n/a	chr8:125576737-125576750
2	CTCF	chr8:125576640-125576790	GM12873	blood:	n/a	chr8:125576737-125576750
3	CTCF	chr8:125576540-125576690	GM12870	blood:	n/a	n/a
4	CTCF	chr8:125576680-125576830	GM06990	blood:	n/a	chr8:125576737-125576750
5	RAD21	chr8:125576601-125576879	K562	blood:	n/a	n/a
6	CTCF	chr8:125576680-125576814	GM10248	blood:	n/a	chr8:125576737-125576750
7	CTCF	chr8:125576638-125576924	GM12878	blood:	n/a	chr8:125576737-125576750
8	CTCF	chr8:125576660-125576810	GM12864	blood:	n/a	chr8:125576737-125576750
9	CTCF	chr8:125576680-125576830	AG04449	skin:	n/a	chr8:125576737-125576750
10	ZC3H11A	chr8:125576628-125577033	K562	blood:	n/a	n/a
11	CTCF	chr8:125576655-125576843	GM12892	blood:	n/a	chr8:125576737-125576750
12	MAZ	chr8:125576601-125577143	K562	blood:	n/a	n/a
13	CTCF	chr8:125576660-125576810	HPF	lung:	n/a	chr8:125576737-125576750
14	RAD21	chr8:125576558-125576840	GM12878	blood:	n/a	n/a
15	CTCF	chr8:125576660-125576810	GM12874	blood:	n/a	chr8:125576737-125576750
16	CTCF	chr8:125576580-125576730	AoAF	blood vessel:	n/a	n/a
17	CTCF	chr8:125576660-125576810	GM12871	blood:	n/a	chr8:125576737-125576750
18	CTCF	chr8:125576655-125576823	K562	blood:	n/a	chr8:125576737-125576750
19	CTCF	chr8:125576660-125576848	GM12891	blood:	n/a	chr8:125576737-125576750
20	CTCF	chr8:125576600-125576750	GM12874	blood:	n/a	chr8:125576737-125576750
21	CTCF	chr8:125576660-125576810	GM12875	blood:	n/a	chr8:125576737-125576750
22	CTCF	chr8:125576584-125576895	IMR90	lung:	n/a	chr8:125576737-125576750
23	CTCF	chr8:125576674-125576787	GM13976	blood:	n/a	chr8:125576737-125576750
24	CTCF	chr8:125576640-125576790	AG04450	lung:	n/a	chr8:125576737-125576750
25	CTCF	chr8:125576580-125576942	K562	blood:	n/a	chr8:125576737-125576750
26	CTCF	chr8:125576660-125576810	GM12866	blood:	n/a	chr8:125576737-125576750
27	SMC3	chr8:125576603-125576905	K562	blood:	n/a	chr8:125576736-125576750
28	CTCF	chr8:125576660-125576810	GM12872	blood:	n/a	chr8:125576737-125576750
29	CTCF	chr8:125576660-125576810	AG10803	skin:	n/a	chr8:125576737-125576750
30	CTCF	chr8:125576620-125576770	GM12801	blood:	n/a	chr8:125576737-125576750
31	CTCF	chr8:125576640-125576790	GM12869	blood:	n/a	chr8:125576737-125576750
32	CTCF	chr8:125576660-125576810	HMF	breast:	n/a	chr8:125576737-125576750
33	CTCF	chr8:125576639-125576860	GM19240	blood:	n/a	chr8:125576737-125576750
34	CTCF	chr8:125576660-125576810	GM12873	blood:	n/a	chr8:125576737-125576750
35	CTCF	chr8:125576634-125576839	GM19238	blood:	n/a	chr8:125576737-125576750
36	CTCF	chr8:125576680-125576830	HCPEpiC	choroid plexus:	n/a	chr8:125576737-125576750
37	CTCF	chr8:125576644-125576800	GM20000	blood:	n/a	chr8:125576737-125576750
38	RAD21	chr8:125576594-125576855	GM12878	blood:	n/a	n/a
39	RAD21	chr8:125576628-125576786	K562	blood:	n/a	n/a
40	CTCF	chr8:125576640-125576790	GM12864	blood:	n/a	chr8:125576737-125576750
41	CTCF	chr8:125576600-125576750	GM12872	blood:	n/a	chr8:125576737-125576750
42	CTCF	chr8:125576620-125576770	HA-sp	spinal cord:	n/a	chr8:125576737-125576750
43	CTCF	chr8:125576619-125576842	Spleen_OC	spleen:	n/a	chr8:125576737-125576750
44	CTCF	chr8:125576600-125576750	HUVEC	blood vessel:	n/a	chr8:125576737-125576750
45	CTCF	chr8:125576457-125577006	K562	blood:	n/a	chr8:125576737-125576750
46	ZMIZ1	chr8:125576650-125577161	K562	blood:	n/a	n/a
47	CTCF	chr8:125576600-125576750	HBMEC	blood vessel:	n/a	chr8:125576737-125576750
48	CTCF	chr8:125576680-125576830	GM12867	blood:	n/a	chr8:125576737-125576750
49	CTCF	chr8:125576660-125576810	GM12868	blood:	n/a	chr8:125576737-125576750
50	CTCF	chr8:125576660-125576810	BJ	skin:	n/a	chr8:125576737-125576750

No.	Distal block	Cell Line	Cell type
1	chr8:125560928..125566588-chr8:125566852..125577107,17	MCF-7	breast:
2	chr8:125549460..125555106-chr8:125573452..125578755,9	MCF-7	breast:
3	chr8:125573757..125577202-chr8:125578987..125583404,3	MCF-7	breast:
4	chr8:125548205..125551096-chr8:125575812..125578141,2	MCF-7	breast:
5	chr8:125575430..125576994-chr8:125827635..125829466,2	K562	blood:
6	chr8:125486165..125488789-chr8:125574025..125577553,3	MCF-7	breast:
7	chr8:125576007..125577952-chr8:125590257..125591907,2	MCF-7	breast:
8	chr8:125572972..125577628-chr8:125578200..125582090,6	MCF-7	breast:
9	chr8:125574370..125578079-chr8:125630160..125632086,3	MCF-7	breast:
10	chr8:125567601..125570100-chr8:125573465..125576752,3	MCF-7	breast:

Variant related genes	Relation type
MTSS1	TF binding region
ENSG00000147684	Chromatin interaction
ENSG00000170881	Chromatin interaction
ENSG00000147687	Chromatin interaction
ENSG00000170873	Chromatin interaction
ENSG00000272486	Chromatin interaction
ENSG00000255491	Chromatin interaction
ENSG00000245149	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10505446	0.93[CEU][hapmap]
rs13263130	1.00[LWK][hapmap];0.80[MKK][hapmap]
rs13269215	1.00[LWK][hapmap]
rs17298759	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17298884	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17298912	0.93[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299030	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17300503	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17372350	1.00[CEU][hapmap]
rs17372901	1.00[ASW][hapmap];0.86[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[ASN][1000 genomes]
rs4286935	0.86[CEU][hapmap]
rs4457314	1.00[LWK][hapmap];0.80[MKK][hapmap]
rs4585740	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6470248	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7003602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7010902	1.00[LWK][hapmap]
rs7830235	0.92[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv1024804	chr8:125575803-125600950	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17299208	TRMT12	cis	cerebellum	SCAN
rs17299208	A1BG	trans	parietal	SCAN
rs17299208	ZNF572	cis	cerebellum	SCAN
rs17299208	TRMT12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
2	chr8:125556800-125576800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr8:125564400-125576800	Strong transcription	Fetal Intestine Small	intestine
4	chr8:125566000-125602400	Weak transcription	Aorta	Aorta
5	chr8:125566200-125590400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:125566400-125577600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr8:125566400-125577800	Weak transcription	Small Intestine	intestine
8	chr8:125566400-125600600	Weak transcription	NHEK	skin
9	chr8:125566600-125577200	Weak transcription	Osteobl	bone
10	chr8:125566800-125581400	Weak transcription	HSMM	muscle
11	chr8:125567000-125590200	Weak transcription	Fetal Brain Male	brain
12	chr8:125568200-125577000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr8:125570000-125584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr8:125570800-125605000	Weak transcription	Colon Smooth Muscle	Colon
15	chr8:125571800-125581200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr8:125572000-125577000	Weak transcription	NHLF	lung
17	chr8:125574200-125577200	Enhancers	Psoas Muscle	Psoas
18	chr8:125574400-125609400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr8:125574800-125580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:125574800-125581000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr8:125574800-125590200	Weak transcription	HMEC	breast
22	chr8:125575200-125576800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr8:125575200-125576800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr8:125575200-125577200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr8:125575200-125577400	Enhancers	Left Ventricle	heart
26	chr8:125575200-125578000	Genic enhancers	Fetal Muscle Leg	muscle
27	chr8:125575200-125578200	Enhancers	Lung	lung
28	chr8:125575200-125578800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr8:125575400-125577200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr8:125575400-125577400	Weak transcription	Gastric	stomach
31	chr8:125575400-125589200	Weak transcription	Esophagus	oesophagus
32	chr8:125575600-125576800	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr8:125575600-125576800	Enhancers	Brain Cingulate Gyrus	brain
34	chr8:125575600-125576800	Genic enhancers	Fetal Stomach	stomach
35	chr8:125575600-125577200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr8:125575600-125577200	Genic enhancers	Brain Inferior Temporal Lobe	brain
37	chr8:125575600-125577400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr8:125575600-125577600	Enhancers	Duodenum Mucosa	Duodenum
39	chr8:125575600-125577600	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr8:125575600-125577800	Enhancers	Adipose Nuclei	Adipose
41	chr8:125575600-125577800	Enhancers	Stomach Mucosa	stomach
42	chr8:125575600-125578400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr8:125575600-125600600	Weak transcription	Fetal Kidney	kidney
44	chr8:125575800-125577000	Enhancers	Spleen	Spleen
45	chr8:125575800-125577200	Weak transcription	Brain Germinal Matrix	brain
46	chr8:125575800-125577400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr8:125575800-125577400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr8:125575800-125577600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr8:125575800-125577600	Enhancers	Brain Substantia Nigra	brain
50	chr8:125575800-125577600	Flanking Active TSS	Dnd41	blood

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