Variant report

Variant	rs11714060
Chromosome Location	chr3:143567207-143567208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143566553..143569042-chr3:143690803..143692633,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAQR9-7	chr3:143566990-143567311	NONHSAT092530

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10433436	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319100	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319101	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1394398	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1394402	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1979911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995529	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995530	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2011290	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2361202	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2361203	0.94[EUR][1000 genomes]
rs2361205	0.94[EUR][1000 genomes]
rs2361206	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2361207	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2361208	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361209	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2885193	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2885194	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2885195	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4286430	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4499594	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839612	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839671	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4839672	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839674	1.00[CEU][hapmap]
rs6440195	1.00[CEU][hapmap]
rs6440196	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs6768702	1.00[EUR][1000 genomes]
rs6780027	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6782974	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs7623477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7627020	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629598	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9289669	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9822158	1.00[MEX][hapmap]
rs9824974	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836851	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9841753	1.00[MEX][hapmap]
rs9870661	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143563200-143567600	Active TSS	GM12878-XiMat	blood
2	chr3:143565200-143567400	Active TSS	Placenta	Placenta
3	chr3:143565200-143567400	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr3:143565400-143567600	Active TSS	Brain Hippocampus Middle	brain
5	chr3:143565400-143567600	Active TSS	Stomach Smooth Muscle	stomach
6	chr3:143565400-143567600	Active TSS	NHDF-Ad	bronchial
7	chr3:143565800-143567400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:143565800-143567400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:143565800-143567400	Active TSS	Liver	Liver
10	chr3:143565800-143567400	Active TSS	NHLF	lung
11	chr3:143565800-143567600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:143565800-143567600	Active TSS	Primary T cells fromperipheralblood	blood
13	chr3:143565800-143567600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:143565800-143567600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:143565800-143567600	Active TSS	Duodenum Mucosa	Duodenum
16	chr3:143565800-143567600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr3:143565800-143567600	Active TSS	Fetal Stomach	stomach
18	chr3:143565800-143567600	Active TSS	Psoas Muscle	Psoas
19	chr3:143565800-143567600	Active TSS	Right Atrium	heart
20	chr3:143565800-143567800	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:143565800-143569200	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr3:143566000-143567400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:143566000-143567400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:143566000-143567400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:143566000-143567400	Active TSS	Fetal Intestine Small	intestine
26	chr3:143566000-143567400	Active TSS	Fetal Thymus	thymus
27	chr3:143566000-143567400	Active TSS	Thymus	Thymus
28	chr3:143566000-143567600	Active TSS	Brain Substantia Nigra	brain
29	chr3:143566000-143567600	Active TSS	Colon Smooth Muscle	Colon
30	chr3:143566000-143567600	Active TSS	Fetal Muscle Leg	muscle
31	chr3:143566000-143567800	Flanking Active TSS	Dnd41	blood
32	chr3:143566000-143568200	Active TSS	Brain Anterior Caudate	brain
33	chr3:143566000-143568400	Active TSS	Ovary	ovary
34	chr3:143566200-143567400	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr3:143566200-143567400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr3:143566200-143567400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:143566200-143567400	Active TSS	Adipose Nuclei	Adipose
38	chr3:143566200-143567400	Active TSS	Brain Germinal Matrix	brain
39	chr3:143566200-143567400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr3:143566200-143567400	Active TSS	Fetal Intestine Large	intestine
41	chr3:143566200-143567400	Active TSS	Fetal Muscle Trunk	muscle
42	chr3:143566200-143567400	Active TSS	Rectal Smooth Muscle	rectum
43	chr3:143566200-143567600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:143566200-143567600	Active TSS	Brain Angular Gyrus	brain
45	chr3:143566200-143567600	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr3:143566200-143567600	Active TSS	Fetal Lung	lung
47	chr3:143566200-143567800	Active TSS	Fetal Kidney	kidney
48	chr3:143566200-143568000	Active TSS	Brain Cingulate Gyrus	brain
49	chr3:143566200-143568600	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr3:143566400-143567400	Active TSS	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links