Variant report

Variant	rs62149297
Chromosome Location	chr2:100585484-100585485
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	chr2:100577188..100580714-chr2:100582263..100586787,5	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10165066	0.88[EUR][1000 genomes]
rs10183465	0.89[EUR][1000 genomes]
rs10187195	0.89[EUR][1000 genomes]
rs10189707	0.88[EUR][1000 genomes]
rs10198187	0.89[EUR][1000 genomes]
rs10209198	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11887136	0.88[EUR][1000 genomes]
rs11897706	0.85[EUR][1000 genomes]
rs13382597	0.88[EUR][1000 genomes]
rs13383014	0.89[EUR][1000 genomes]
rs13393937	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13405987	0.88[EUR][1000 genomes]
rs13410695	0.89[EUR][1000 genomes]
rs13410884	0.90[EUR][1000 genomes]
rs13413309	0.86[EUR][1000 genomes]
rs13416574	0.88[EUR][1000 genomes]
rs1574207	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17352514	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17436955	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17436983	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17437101	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2001722	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4129805	0.88[EUR][1000 genomes]
rs4485586	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4632399	0.80[EUR][1000 genomes]
rs4641993	0.85[EUR][1000 genomes]
rs56332326	0.88[EUR][1000 genomes]
rs57360658	0.84[EUR][1000 genomes]
rs58270548	0.92[EUR][1000 genomes]
rs62147652	0.94[EUR][1000 genomes]
rs62147658	0.96[EUR][1000 genomes]
rs62147659	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62149260	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62149262	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62149263	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62149264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62149268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62149270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62149271	0.88[EUR][1000 genomes]
rs62149272	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62149296	0.88[EUR][1000 genomes]
rs62149298	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62149299	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62149301	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62149302	0.88[EUR][1000 genomes]
rs62149303	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62149304	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62149305	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62149307	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62149310	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62149311	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62149314	0.82[EUR][1000 genomes]
rs6719214	0.86[EUR][1000 genomes]
rs72819146	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72819147	0.88[EUR][1000 genomes]
rs72819148	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72819149	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72819157	0.89[EUR][1000 genomes]
rs7425132	0.86[EUR][1000 genomes]
rs7576469	0.89[EUR][1000 genomes]
rs7577040	0.84[EUR][1000 genomes]
rs9308831	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1003114	chr2:100480432-100601586	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100550800-100618200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:100563200-100625400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:100564800-100617000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:100570600-100598400	Weak transcription	Dnd41	blood
5	chr2:100573800-100599600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:100574400-100591000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:100577200-100590800	Weak transcription	Fetal Kidney	kidney
8	chr2:100577400-100618200	Weak transcription	Aorta	Aorta
9	chr2:100577600-100587000	Weak transcription	Lung	lung
10	chr2:100577800-100603400	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:100577800-100607400	Weak transcription	Thymus	Thymus
12	chr2:100577800-100623000	Weak transcription	Adipose Nuclei	Adipose
13	chr2:100577800-100623000	Weak transcription	Brain Angular Gyrus	brain
14	chr2:100578000-100589600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:100578000-100616200	Weak transcription	Fetal Thymus	thymus
16	chr2:100578400-100589000	Weak transcription	Fetal Brain Female	brain
17	chr2:100578400-100591000	Weak transcription	Fetal Brain Male	brain
18	chr2:100578800-100588800	Weak transcription	Fetal Lung	lung
19	chr2:100578800-100589200	Weak transcription	Gastric	stomach
20	chr2:100580600-100586000	Strong transcription	Primary B cells from cord blood	blood
21	chr2:100582400-100608000	Weak transcription	Fetal Stomach	stomach
22	chr2:100583200-100608000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr2:100583800-100585800	Strong transcription	Primary hematopoietic stem cells	blood
24	chr2:100583800-100586200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:100584000-100585800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:100584000-100586000	Strong transcription	Primary T cells from cord blood	blood
27	chr2:100585200-100585800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links