Variant report

Variant	rs2765269
Chromosome Location	chr1:62761764-62761765
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:62759279..62761889-chr1:62763662..62766108,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201153	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10157938	0.83[ASN][1000 genomes]
rs10465842	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493318	0.90[JPT][hapmap]
rs10889318	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11207955	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs11207956	0.90[JPT][hapmap]
rs12031176	0.86[JPT][hapmap]
rs12038843	0.90[JPT][hapmap]
rs12127630	0.81[JPT][hapmap]
rs12138544	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12749514	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325740	0.89[ASN][1000 genomes]
rs1886833	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1886834	0.81[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1925827	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2366207	0.98[ASN][1000 genomes]
rs2477874	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2765266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35126231	0.98[ASN][1000 genomes]
rs3850629	0.82[JPT][hapmap]
rs3850632	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs3861936	0.89[JPT][hapmap]
rs4915606	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587966	0.87[ASN][1000 genomes]
rs6658312	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675508	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6675627	0.89[ASN][1000 genomes]
rs7514266	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881548	0.80[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs9803815	0.90[JPT][hapmap]

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	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	nsv431712	chr1:62759369-62766001	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62754400-62773400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:62754800-62765200	Weak transcription	Fetal Heart	heart
3	chr1:62756200-62765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:62756400-62764800	Weak transcription	HepG2	liver
5	chr1:62759800-62761800	Enhancers	Fetal Muscle Trunk	muscle
6	chr1:62759800-62765400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:62759800-62770800	Enhancers	Fetal Muscle Leg	muscle
8	chr1:62760000-62762400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:62760400-62762000	Enhancers	Brain Angular Gyrus	brain
10	chr1:62760400-62762400	Enhancers	Primary T cells from cord blood	blood
11	chr1:62760400-62762400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr1:62760800-62761800	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:62760800-62762400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:62761000-62761800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:62761000-62761800	Enhancers	HSMM	muscle
16	chr1:62761000-62762000	Enhancers	H9 Cell Line	embryonic stem cell
17	chr1:62761000-62762000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:62761000-62762200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr1:62761000-62762200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:62761000-62762200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr1:62761000-62762400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:62761000-62762400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:62761000-62762400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:62761000-62763200	Enhancers	Fetal Stomach	stomach
25	chr1:62761200-62761800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr1:62761200-62761800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:62761200-62761800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:62761200-62761800	Enhancers	Adipose Nuclei	Adipose
29	chr1:62761200-62761800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr1:62761200-62761800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr1:62761200-62762000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:62761200-62762000	Enhancers	Colonic Mucosa	Colon
33	chr1:62761200-62762000	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr1:62761200-62762200	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr1:62761200-62762200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:62761200-62762200	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr1:62761200-62762200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr1:62761200-62762200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr1:62761200-62762200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:62761200-62762200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:62761200-62762200	Enhancers	Fetal Lung	lung
42	chr1:62761200-62762200	Enhancers	Placenta	Placenta
43	chr1:62761200-62762200	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr1:62761200-62762200	Enhancers	HSMMtube	muscle
45	chr1:62761200-62762200	Enhancers	NH-A	brain
46	chr1:62761200-62762200	Enhancers	NHDF-Ad	bronchial
47	chr1:62761200-62762200	Enhancers	NHEK	skin
48	chr1:62761200-62762400	Enhancers	Primary hematopoietic stem cells	blood
49	chr1:62761200-62762400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
50	chr1:62761200-62762400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links