Variant report

Variant	rs13269215
Chromosome Location	chr8:125565978-125565979
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125557600..125560665-chr8:125561474..125566163,6	MCF-7	breast:
2	chr8:125565320..125567312-chr8:125567324..125569326,2	MCF-7	breast:
3	chr8:125542543..125545366-chr8:125564681..125567341,2	MCF-7	breast:
4	chr8:125557359..125560396-chr8:125563953..125566035,3	MCF-7	breast:
5	chr8:125563772..125566643-chr8:125826415..125829140,2	K562	blood:
6	chr8:125560928..125566588-chr8:125566852..125577107,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170873	Chromatin interaction
ENSG00000255491	Chromatin interaction
ENSG00000147684	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1131024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13250890	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13254054	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13263130	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13264071	0.87[CEU][hapmap];1.00[GIH][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs13276295	0.86[CEU][hapmap];0.91[GIH][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17298010	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17298759	1.00[LWK][hapmap]
rs17299208	1.00[LWK][hapmap]
rs17372901	1.00[LWK][hapmap]
rs34008273	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34115246	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34681068	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34684627	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34714561	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35135081	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35309726	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35419095	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4358788	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4457314	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4535724	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4540394	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7010902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7813473	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13269215	TRMT12	cis	cerebellum	SCAN
rs13269215	NSMCE2	cis	cerebellum	SCAN
rs13269215	ZNF572	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125552200-125568600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:125553400-125568000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:125553400-125568200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr8:125553400-125575200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr8:125553400-125575200	Strong transcription	Fetal Muscle Leg	muscle
6	chr8:125553600-125566400	Strong transcription	A549	lung
7	chr8:125553600-125566800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr8:125553800-125575400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr8:125553800-125581200	Strong transcription	Fetal Brain Female	brain
10	chr8:125554000-125572400	Strong transcription	Thymus	Thymus
11	chr8:125554000-125574000	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr8:125554200-125566800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr8:125554200-125568600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr8:125554200-125570000	Strong transcription	Fetal Thymus	thymus
15	chr8:125554200-125576200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr8:125554400-125567400	Strong transcription	Colon Smooth Muscle	Colon
17	chr8:125554400-125568200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr8:125554400-125568400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr8:125554400-125569000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr8:125554400-125574200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr8:125554400-125575400	Strong transcription	Primary B cells from cord blood	blood
22	chr8:125554400-125576200	Strong transcription	Fetal Intestine Large	intestine
23	chr8:125554600-125566400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr8:125554600-125566400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr8:125554600-125566600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr8:125554600-125566600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr8:125554600-125568000	Strong transcription	Rectal Smooth Muscle	rectum
28	chr8:125554600-125574000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr8:125554600-125575000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr8:125554600-125575800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr8:125554800-125566800	Strong transcription	HSMM	muscle
32	chr8:125554800-125569200	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr8:125555000-125566600	Strong transcription	NHLF	lung
34	chr8:125555000-125568200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr8:125555200-125566400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr8:125555200-125566400	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr8:125555200-125566600	Strong transcription	Fetal Kidney	kidney
38	chr8:125555200-125569000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr8:125555200-125574000	Strong transcription	Placenta	Placenta
40	chr8:125555200-125575000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr8:125555200-125575200	Strong transcription	Brain Cingulate Gyrus	brain
42	chr8:125555400-125566400	Strong transcription	NHEK	skin
43	chr8:125555400-125568200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr8:125555600-125567000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr8:125555600-125574200	Strong transcription	Primary T cells from cord blood	blood
46	chr8:125555800-125566600	Strong transcription	HMEC	breast
47	chr8:125556000-125574200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr8:125556200-125566000	Strong transcription	GM12878-XiMat	blood
49	chr8:125556200-125575000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr8:125556600-125566400	Strong transcription	Dnd41	blood

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