Variant report

Variant	rs12055697
Chromosome Location	chr6:25303100-25303101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25277631..25279275-chr6:25301822..25304144,2	MCF-7	breast:
2	chr6:25302209..25304566-chr6:25321319..25323421,2	MCF-7	breast:
3	chr6:25279234..25282196-chr6:25302311..25304060,2	K562	blood:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs16890366	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1883393	1.00[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs2143023	0.88[ASN][1000 genomes]
rs2690042	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2744287	0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4712904	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712905	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4712906	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4712907	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs55967593	0.88[ASN][1000 genomes]
rs55999195	0.88[ASN][1000 genomes]
rs58191968	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs60084615	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6456664	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6456665	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6456666	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6456668	0.87[ASN][1000 genomes]
rs6903148	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6906812	0.87[ASN][1000 genomes]
rs6913606	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6913886	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6914439	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6914514	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6914654	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6914798	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6914930	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6915270	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6917631	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6921343	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6923529	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6927238	0.84[ASN][1000 genomes]
rs6938281	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6938594	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs730711	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73392399	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73396126	0.87[ASN][1000 genomes]
rs7741580	0.87[ASN][1000 genomes]
rs7743750	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7746942	0.87[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7746969	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7755701	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7756143	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7758529	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7759796	0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs7759879	0.87[ASN][1000 genomes]
rs7760067	0.88[ASN][1000 genomes]
rs7760151	0.88[ASN][1000 genomes]
rs7764111	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs9295654	0.87[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9348671	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9356974	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9356975	0.89[JPT][hapmap]
rs9366616	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9379752	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9379753	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9379754	0.94[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap]
rs9393639	0.88[ASN][1000 genomes]
rs9461132	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9461134	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9461135	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9461136	0.80[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9467466	0.87[ASW][hapmap];0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs999039	0.81[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25290400-25313400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:25294200-25311200	Weak transcription	Lung	lung
3	chr6:25297200-25303200	Weak transcription	Primary T cells from cord blood	blood
4	chr6:25297400-25304600	Weak transcription	Left Ventricle	heart
5	chr6:25298000-25303200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:25298000-25311800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:25298600-25303400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:25300600-25303200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr6:25300600-25303600	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr6:25300600-25304000	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:25300800-25303400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:25300800-25304000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr6:25301000-25304000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:25301200-25303200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr6:25301200-25303800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr6:25301200-25303800	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:25301200-25305400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr6:25301400-25303400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr6:25301400-25303800	Enhancers	Primary B cells from cord blood	blood
20	chr6:25301400-25313400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:25301600-25303400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:25301600-25304200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:25301600-25311600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:25301800-25304200	Enhancers	NHLF	lung
25	chr6:25301800-25305600	Enhancers	Fetal Intestine Large	intestine
26	chr6:25301800-25306000	Enhancers	Fetal Intestine Small	intestine
27	chr6:25302000-25303200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:25302000-25303200	Enhancers	Fetal Heart	heart
29	chr6:25302000-25312800	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:25302200-25303200	Enhancers	Brain Anterior Caudate	brain
31	chr6:25302200-25303400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr6:25302200-25303400	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr6:25302200-25303400	Enhancers	Brain Germinal Matrix	brain
34	chr6:25302400-25303200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:25302400-25303200	Enhancers	Ovary	ovary
36	chr6:25302400-25303400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:25302400-25303400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr6:25302400-25303400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr6:25302400-25303800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:25302400-25303800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:25302400-25303800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:25302400-25303800	Enhancers	Brain Angular Gyrus	brain
43	chr6:25302400-25303800	Enhancers	HepG2	liver
44	chr6:25302400-25303800	Enhancers	NH-A	brain
45	chr6:25302400-25304000	Enhancers	Stomach Mucosa	stomach
46	chr6:25302600-25303200	Enhancers	H1 Cell Line	embryonic stem cell
47	chr6:25302600-25303200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:25302600-25303200	Enhancers	Colonic Mucosa	Colon
49	chr6:25302600-25303200	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr6:25302600-25303200	Enhancers	Fetal Thymus	thymus

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