Variant report

Variant	rs13064815
Chromosome Location	chr3:119892121-119892122
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119888337..119890858-chr3:119891647..119894832,5	MCF-7	breast:
2	chr3:119887283..119893170-chr3:119894592..119900399,7	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1079784	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10934520	0.87[AMR][1000 genomes]
rs13061630	1.00[JPT][hapmap]
rs13073885	0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs13079094	0.85[AMR][1000 genomes]
rs1492272	1.00[JPT][hapmap]
rs17813772	1.00[JPT][hapmap]
rs2029607	1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs34014378	0.81[AMR][1000 genomes]
rs34032950	0.89[AMR][1000 genomes]
rs34537735	0.85[AMR][1000 genomes]
rs34720062	0.89[AMR][1000 genomes]
rs34829073	0.81[AMR][1000 genomes]
rs34964758	0.81[AMR][1000 genomes]
rs34998142	0.81[AMR][1000 genomes]
rs35193138	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35280462	0.89[AMR][1000 genomes]
rs35791817	0.87[AMR][1000 genomes]
rs35902169	0.87[AMR][1000 genomes]
rs35977875	0.89[AMR][1000 genomes]
rs4146299	1.00[JPT][hapmap];0.81[TSI][hapmap]
rs4146300	1.00[JPT][hapmap]
rs4676703	1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs4676811	1.00[JPT][hapmap]
rs55871529	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438575	1.00[JPT][hapmap]
rs6776878	1.00[JPT][hapmap]
rs6792814	1.00[JPT][hapmap];0.95[MEX][hapmap]
rs7630226	0.87[AMR][1000 genomes]
rs7633395	0.85[AMR][1000 genomes]
rs7634938	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv829697	chr3:119802856-119918435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
5	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv3967	chr3:119857708-119903115	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv1013788	chr3:119866722-119912297	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	esv3403309	chr3:119892062-119896360	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13064815	KPNA1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119875200-119896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119883200-119895800	Weak transcription	Fetal Intestine Small	intestine
3	chr3:119884800-119895600	Weak transcription	Brain Germinal Matrix	brain
4	chr3:119885000-119895800	Weak transcription	Fetal Lung	lung
5	chr3:119886200-119892400	Strong transcription	Fetal Brain Female	brain
6	chr3:119887200-119895800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:119888400-119892600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:119888400-119895800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:119888400-119895800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:119888400-119896200	Enhancers	NHDF-Ad	bronchial
11	chr3:119888600-119892200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:119888600-119892600	Enhancers	Osteobl	bone
13	chr3:119888600-119893200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:119888600-119896000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:119889400-119893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:119890000-119893000	Weak transcription	A549	lung
17	chr3:119890000-119895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:119890200-119892200	Strong transcription	Fetal Stomach	stomach
19	chr3:119890400-119893600	Weak transcription	Placenta	Placenta
20	chr3:119890400-119895400	Weak transcription	Psoas Muscle	Psoas
21	chr3:119890400-119895800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:119890400-119895800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:119890600-119892200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:119890600-119893600	Weak transcription	Hela-S3	cervix
25	chr3:119890600-119895600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:119890600-119895800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:119890800-119895600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:119890800-119896000	Weak transcription	Right Atrium	heart
29	chr3:119891000-119895800	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:119891200-119893200	Weak transcription	HMEC	breast
31	chr3:119891200-119895600	Weak transcription	Adipose Nuclei	Adipose
32	chr3:119891200-119895600	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:119891400-119895200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:119891400-119895200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:119891400-119895600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:119891400-119895600	Weak transcription	NHLF	lung
37	chr3:119891400-119896200	Weak transcription	Lung	lung
38	chr3:119891600-119892200	ZNF genes & repeats	NHEK	skin
39	chr3:119892000-119892200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:119892000-119892200	Enhancers	HSMMtube	muscle
41	chr3:119892000-119892800	Enhancers	HSMM	muscle
42	chr3:119892000-119895800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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