Variant report

Variant	rs62263056
Chromosome Location	chr3:105388263-105388264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105384518..105386462-chr3:105388169..105391773,3	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs12054270	0.96[ASN][1000 genomes]
rs12487349	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493771	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1443100	0.87[ASN][1000 genomes]
rs16851512	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16851553	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16851673	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1814078	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1867194	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2028598	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2028599	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2055558	0.87[ASN][1000 genomes]
rs2055559	0.87[ASN][1000 genomes]
rs2120104	0.81[ASN][1000 genomes]
rs2301028	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2301034	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2301035	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3213928	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34360428	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35909361	0.83[ASN][1000 genomes]
rs3772517	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3772522	0.96[ASN][1000 genomes]
rs3772525	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3821490	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4431143	0.86[ASN][1000 genomes]
rs4469007	0.86[ASN][1000 genomes]
rs4894956	0.87[ASN][1000 genomes]
rs62255570	0.86[ASN][1000 genomes]
rs62255571	0.86[ASN][1000 genomes]
rs62255572	0.86[ASN][1000 genomes]
rs62255573	0.86[ASN][1000 genomes]
rs62256353	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62258160	0.87[ASN][1000 genomes]
rs62261460	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62261462	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62261487	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62261489	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62261491	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62261492	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62261493	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62261495	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62261496	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62261497	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62261498	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62261499	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62261538	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62261539	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62263057	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62263059	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62263169	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62263170	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62264260	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6765210	0.81[AFR][1000 genomes]
rs6809776	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7619706	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7628896	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7631219	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7641527	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7650046	0.87[ASN][1000 genomes]
rs964173	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9657903	0.86[ASN][1000 genomes]
rs9657924	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs971109	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9849559	0.81[ASN][1000 genomes]
rs9856147	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv877306	chr3:105372196-105495841	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv877307	chr3:105373836-105465189	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv591242	chr3:105373836-105470134	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv877308	chr3:105373836-105495841	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105368800-105388400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:105368800-105393400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:105373000-105419600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:105373400-105401600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:105373600-105419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:105373800-105406200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:105374200-105388400	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:105374200-105392600	Weak transcription	Psoas Muscle	Psoas
9	chr3:105374800-105392800	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:105375000-105395600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:105375200-105395400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:105375200-105395600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:105375800-105389200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:105375800-105399000	Weak transcription	Dnd41	blood
15	chr3:105375800-105405000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:105375800-105419600	Weak transcription	Colonic Mucosa	Colon
17	chr3:105375800-105464600	Weak transcription	Small Intestine	intestine
18	chr3:105376000-105395600	Weak transcription	Esophagus	oesophagus
19	chr3:105376000-105438200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:105376200-105397200	Weak transcription	NHLF	lung
21	chr3:105376400-105395600	Weak transcription	Fetal Brain Male	brain
22	chr3:105376800-105395400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:105376800-105440000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:105377200-105399200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:105378000-105392600	Weak transcription	Ovary	ovary
26	chr3:105378000-105395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:105378000-105420800	Weak transcription	HUVEC	blood vessel
28	chr3:105378000-105455400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:105378600-105438600	Weak transcription	Spleen	Spleen
30	chr3:105378800-105393400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:105379000-105392400	Weak transcription	Fetal Brain Female	brain
32	chr3:105379000-105437400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:105379200-105440400	Weak transcription	Thymus	Thymus
34	chr3:105379600-105391800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:105380600-105411800	Weak transcription	Brain Substantia Nigra	brain
36	chr3:105382200-105404800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:105382400-105392400	Weak transcription	Fetal Kidney	kidney
38	chr3:105382400-105395600	Weak transcription	Pancreas	Pancrea
39	chr3:105382400-105397200	Weak transcription	Lung	lung
40	chr3:105382400-105405000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:105382800-105404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:105383000-105388400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr3:105383800-105398600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:105384200-105400000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:105384600-105404600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:105385000-105389200	Strong transcription	Primary B cells from cord blood	blood
47	chr3:105385000-105390400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:105385000-105404600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:105385200-105388600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:105385200-105398000	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links