Variant report

Variant	rs12270054
Chromosome Location	chr11:65322548-65322549
allele	C/T
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	chr11:65322509-65322571	MCF-7	breast:	n/a	n/a
2	MAZ	chr11:65322367-65323808	IMR90	lung:	n/a	chr11:65323217-65323226 chr11:65323443-65323453 chr11:65323292-65323302
3	SP1	chr11:65322410-65323854	HCT-116	colon:	n/a	chr11:65323444-65323453 chr11:65323291-65323303 chr11:65323292-65323301 chr11:65322833-65322847 chr11:65323288-65323302 chr11:65323291-65323303 chr11:65323443-65323452

No.	Distal block	Cell Line	Cell type
1	chr11:65322009..65324491-chr11:65418105..65419642,2	MCF-7	breast:
2	chr11:65322433..65324295-chr11:65381910..65384762,2	MCF-7	breast:
3	chr11:65322271..65324751-chr6:27776572..27778307,2	MCF-7	breast:
4	chr11:65189010..65195293-chr11:65321323..65327708,15	K562	blood:
5	chr11:65264479..65268560-chr11:65318003..65330456,22	MCF-7	breast:
6	chr11:65184371..65196984-chr11:65316952..65328208,29	K562	blood:

Variant related genes	Relation type
LTBP3	TF binding region
ENSG00000197136	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000173327	Chromatin interaction
ENSG00000203813	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10896009	0.87[MEX][hapmap]
rs10896012	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs10896015	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896016	0.80[JPT][hapmap]
rs11227221	0.80[JPT][hapmap]
rs1143756	0.86[ASN][1000 genomes]
rs1151496	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1151517	0.80[JPT][hapmap]
rs1152619	0.88[TSI][hapmap]
rs1152620	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs11601767	0.80[JPT][hapmap];0.81[TSI][hapmap]
rs1194076	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1194077	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1194104	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12360896	0.87[MEX][hapmap]
rs1346	0.89[CEU][hapmap];0.89[JPT][hapmap]
rs17146964	0.87[MEX][hapmap]
rs1783541	0.83[JPT][hapmap];0.81[MEX][hapmap];0.81[MKK][hapmap]
rs1787663	0.90[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs2510078	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3200401	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs3782091	0.80[JPT][hapmap]
rs4244811	0.80[JPT][hapmap]
rs600231	0.84[TSI][hapmap]
rs67924081	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs947791	0.83[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
4	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
5	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
6	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
7	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
8	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
9	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
10	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
11	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases
12	nsv541075	chr11:65210592-65331136	Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	620 gene(s)	inside rSNPs	diseases
13	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
14	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
15	nsv897721	chr11:65278461-65422853	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
16	nsv897722	chr11:65278461-65436888	Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
17	nsv897723	chr11:65294830-65481166	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
18	nsv897729	chr11:65302893-65322548	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
19	nsv897730	chr11:65302893-65376484	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12270054	CDK2AP2	cis	cerebellum	SCAN
rs12270054	TTC9C	cis	parietal	SCAN
rs12270054	SLC22A10	cis	parietal	SCAN
rs12270054	TPCN2	cis	parietal	SCAN
rs12270054	NEAT1	cis	Nerve Tibial	GTEx
rs12270054	SCGB2A1	cis	cerebellum	SCAN
rs12270054	LTBP3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65307200-65322600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:65309200-65323000	Weak transcription	Psoas Muscle	Psoas
3	chr11:65309400-65323000	Weak transcription	Right Atrium	heart
4	chr11:65310800-65324000	Weak transcription	Fetal Kidney	kidney
5	chr11:65314800-65322800	Weak transcription	NHEK	skin
6	chr11:65318400-65323000	Genic enhancers	Fetal Muscle Trunk	muscle
7	chr11:65318600-65323600	Genic enhancers	Fetal Muscle Leg	muscle
8	chr11:65318600-65325800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr11:65318800-65324600	Enhancers	Primary hematopoietic stem cells	blood
10	chr11:65319000-65323400	Genic enhancers	Fetal Intestine Small	intestine
11	chr11:65319000-65324200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr11:65319000-65324600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr11:65319000-65324600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:65319200-65323200	Weak transcription	Fetal Heart	heart
15	chr11:65319400-65323400	Weak transcription	Brain Substantia Nigra	brain
16	chr11:65319600-65322800	Weak transcription	Ovary	ovary
17	chr11:65319600-65323000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:65320000-65325000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:65320200-65322600	Weak transcription	Left Ventricle	heart
20	chr11:65320400-65322600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:65320400-65322600	Weak transcription	Liver	Liver
22	chr11:65320400-65323000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:65320400-65323000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr11:65320400-65324200	Weak transcription	Aorta	Aorta
25	chr11:65320400-65324600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:65320400-65324600	Enhancers	Fetal Intestine Large	intestine
27	chr11:65320600-65322600	Weak transcription	HepG2	liver
28	chr11:65320800-65322600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:65320800-65322600	Weak transcription	Gastric	stomach
30	chr11:65320800-65322800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:65320800-65324800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:65321000-65322800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr11:65321000-65323000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr11:65321200-65323000	Enhancers	Brain Germinal Matrix	brain
35	chr11:65321200-65324600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:65321200-65324800	Enhancers	Placenta Amnion	Placenta Amnion
37	chr11:65321200-65325400	Enhancers	Fetal Brain Male	brain
38	chr11:65321200-65326200	Enhancers	Spleen	Spleen
39	chr11:65321400-65322600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr11:65321400-65322800	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr11:65321400-65322800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr11:65321400-65322800	Genic enhancers	Stomach Smooth Muscle	stomach
43	chr11:65321400-65323000	Enhancers	NH-A	brain
44	chr11:65321400-65324600	Enhancers	Placenta	Placenta
45	chr11:65321400-65324800	Enhancers	Esophagus	oesophagus
46	chr11:65321600-65322600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr11:65321600-65323000	Enhancers	HSMM	muscle
48	chr11:65321600-65323400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr11:65321600-65324000	Enhancers	HMEC	breast
50	chr11:65321600-65324200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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