Variant report

Variant	rs2490253
Chromosome Location	chr6:80895870-80895871
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	chr1:201223408..201224319-chr6:80895392..80896149,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10943698	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12209624	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1408292	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1575541	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1892475	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2322632	0.82[EUR][1000 genomes]
rs2322635	0.84[ASN][1000 genomes]
rs2476826	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2490239	0.81[EUR][1000 genomes]
rs2490241	0.82[EUR][1000 genomes]
rs2490244	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2490245	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2490250	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2490251	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2505927	0.82[EUR][1000 genomes]
rs2505929	0.82[EUR][1000 genomes]
rs2505932	0.82[EUR][1000 genomes]
rs2505935	0.81[EUR][1000 genomes]
rs2505939	0.82[EUR][1000 genomes]
rs2505940	0.82[EUR][1000 genomes]
rs2505942	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2505944	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3805911	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3805913	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3805919	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3828753	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4256394	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6938280	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs742833	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7741013	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7745301	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7746917	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9294172	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9448911	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830708	chr6:80844283-80996876	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1034096	chr6:80856135-81150170	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv886309	chr6:80880138-80959885	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv886310	chr6:80880138-81025879	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv932996	chr6:80880896-81134991	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv497995	chr6:80883701-81134991	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1033452	chr6:80888667-81000213	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80842200-80914200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:80855200-80907000	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:80855200-80907200	Weak transcription	Ovary	ovary
4	chr6:80855800-80896000	Weak transcription	Aorta	Aorta
5	chr6:80863200-80907200	Weak transcription	Psoas Muscle	Psoas
6	chr6:80874200-80899200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:80878000-80921000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr6:80878600-80916000	Weak transcription	Adipose Nuclei	Adipose
9	chr6:80878800-80907200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:80878800-80914200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:80880600-80914200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr6:80882000-80896200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:80882400-80935400	Weak transcription	Dnd41	blood
14	chr6:80883800-80913200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr6:80885800-80919000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:80886000-80899000	Weak transcription	Liver	Liver
17	chr6:80891400-80907200	Weak transcription	Left Ventricle	heart
18	chr6:80891600-80896000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:80891600-80898000	Weak transcription	Pancreas	Pancrea
20	chr6:80891600-80907400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:80891600-80931200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr6:80892200-80913400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:80893000-80907400	Weak transcription	HSMM	muscle
24	chr6:80895000-80897800	Weak transcription	Primary T cells from cord blood	blood
25	chr6:80895200-80896400	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr6:80895400-80896000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr6:80895400-80896200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:80895400-80896200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:80895400-80896200	ZNF genes & repeats	Fetal Stomach	stomach
30	chr6:80895400-80896400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:80895400-80896400	Enhancers	HMEC	breast
32	chr6:80895400-80896600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:80895600-80896000	Weak transcription	Lung	lung
34	chr6:80895600-80896400	Enhancers	NHEK	skin
35	chr6:80895800-80896000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:80895800-80896200	Enhancers	Esophagus	oesophagus
37	chr6:80895800-80896400	Enhancers	Right Ventricle	heart

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