Variant report

Variant	rs10042569
Chromosome Location	chr5:108195410-108195411
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	chr5:108193098..108195960-chr5:108197076..108199919,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10036583	1.00[JPT][hapmap]
rs10037675	1.00[JPT][hapmap]
rs10039132	1.00[JPT][hapmap]
rs10039544	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10039951	1.00[JPT][hapmap]
rs10041657	1.00[JPT][hapmap]
rs10042152	1.00[JPT][hapmap]
rs10050547	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10052208	1.00[JPT][hapmap]
rs10052531	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10054086	1.00[JPT][hapmap]
rs10061811	1.00[JPT][hapmap]
rs10064960	1.00[JPT][hapmap]
rs10065605	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10065611	1.00[JPT][hapmap]
rs10070327	1.00[JPT][hapmap]
rs10072148	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10077917	1.00[JPT][hapmap]
rs10223256	0.82[JPT][hapmap]
rs10477428	1.00[JPT][hapmap]
rs10477429	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10477432	1.00[JPT][hapmap]
rs10477931	1.00[JPT][hapmap]
rs10477933	0.82[CHD][hapmap]
rs11741855	1.00[JPT][hapmap]
rs11748534	1.00[JPT][hapmap]
rs12719099	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs13358881	1.00[JPT][hapmap]
rs13359423	1.00[JPT][hapmap]
rs13360253	1.00[JPT][hapmap]
rs1396444	1.00[JPT][hapmap]
rs1423456	1.00[JPT][hapmap]
rs1423459	1.00[JPT][hapmap]
rs17161466	0.83[ASW][hapmap];1.00[JPT][hapmap]
rs17161505	1.00[JPT][hapmap]
rs17161540	1.00[JPT][hapmap]
rs17161562	1.00[JPT][hapmap]
rs17163941	1.00[JPT][hapmap]
rs2009646	1.00[JPT][hapmap]
rs2081128	1.00[JPT][hapmap]
rs2113001	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2229085	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs28718068	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2900037	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs35141056	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs3805600	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs3805601	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs41508849	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4358573	1.00[JPT][hapmap]
rs4361568	1.00[JPT][hapmap]
rs4479887	1.00[JPT][hapmap]
rs4560594	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs4560595	1.00[JPT][hapmap]
rs61328923	0.81[ASN][1000 genomes]
rs6594341	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6869591	1.00[JPT][hapmap]
rs6873130	1.00[JPT][hapmap]
rs6873917	1.00[JPT][hapmap]
rs6884637	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6888173	1.00[JPT][hapmap]
rs6889965	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709144	0.90[CHD][hapmap]
rs7711892	1.00[JPT][hapmap]
rs7715658	1.00[JPT][hapmap]
rs7719329	0.82[JPT][hapmap]
rs7724385	0.82[CHD][hapmap]
rs7728920	1.00[JPT][hapmap]
rs889269	1.00[JPT][hapmap]
rs9326750	1.00[JPT][hapmap]
rs9326752	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs9326753	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9885265	1.00[JPT][hapmap]

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	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv471039	chr5:108133967-108245089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv1801555	chr5:108166720-108203055	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108147000-108198800	Weak transcription	Aorta	Aorta
2	chr5:108147000-108208800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr5:108166400-108203200	Weak transcription	HSMM	muscle
4	chr5:108166600-108217000	Weak transcription	Left Ventricle	heart
5	chr5:108167200-108220400	Weak transcription	Fetal Lung	lung
6	chr5:108168200-108203800	Weak transcription	Adipose Nuclei	Adipose
7	chr5:108169400-108229200	Weak transcription	Fetal Stomach	stomach
8	chr5:108173000-108199800	Weak transcription	Brain Angular Gyrus	brain
9	chr5:108173400-108239800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:108179800-108199800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:108179800-108202000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:108182000-108217000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:108183800-108260400	Weak transcription	Ovary	ovary
14	chr5:108187200-108202600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:108187200-108204600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:108187200-108211800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:108187800-108199200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:108190600-108200000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:108194000-108217000	Weak transcription	Esophagus	oesophagus
20	chr5:108194200-108203000	Weak transcription	NHLF	lung
21	chr5:108194400-108195600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:108194600-108260000	Weak transcription	Fetal Intestine Large	intestine
23	chr5:108194800-108200000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr5:108194800-108204200	Weak transcription	NHEK	skin
25	chr5:108194800-108204600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:108194800-108207000	Weak transcription	HUVEC	blood vessel
27	chr5:108194800-108208600	Weak transcription	Osteobl	bone
28	chr5:108194800-108236200	Weak transcription	Hela-S3	cervix
29	chr5:108195000-108204800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:108195000-108211800	Weak transcription	NHDF-Ad	bronchial
31	chr5:108195200-108197600	Weak transcription	Fetal Brain Male	brain
32	chr5:108195200-108203400	Weak transcription	Primary B cells from cord blood	blood
33	chr5:108195200-108204800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:108195200-108206600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr5:108195200-108209000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr5:108195200-108211000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr5:108195200-108231600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr5:108195200-108231600	Weak transcription	Psoas Muscle	Psoas
39	chr5:108195200-108234400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr5:108195400-108202600	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links