Variant report

Variant	rs13059128
Chromosome Location	chr3:141171190-141171191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:140910735..140911727-chr3:141170663..141171495,2	K562	blood:
2	chr3:141022868..141024851-chr3:141170597..141172187,2	MCF-7	breast:
3	chr3:141078410..141082494-chr3:141170544..141172496,3	MCF-7	breast:
4	chr3:141025929..141033510-chr3:141171081..141179408,10	MCF-7	breast:
5	chr3:141026506..141030618-chr3:141169234..141171603,4	MCF-7	breast:
6	chr3:141169931..141172145-chr3:141175203..141179161,4	K562	blood:
7	chr3:141030674..141032798-chr3:141168575..141172474,3	K562	blood:
8	chr3:141163698..141166261-chr3:141168947..141171763,3	MCF-7	breast:
9	chr3:141030343..141031265-chr3:141170565..141171975,8	K562	blood:
10	chr3:141084098..141087550-chr3:141168152..141171297,3	MCF-7	breast:
11	chr3:141164105..141165870-chr3:141170632..141173126,2	K562	blood:
12	chr3:140949389..140951483-chr3:141169503..141172131,2	K562	blood:
13	chr3:141030383..141031255-chr3:141170825..141171481,2	MCF-7	breast:
14	chr3:141029632..141032040-chr3:141170273..141172073,2	K562	blood:
15	chr3:141169710..141171431-chr3:141177334..141179161,2	K562	blood:
16	chr3:141164105..141166380-chr3:141168817..141173824,4	K562	blood:
17	chr3:141030604..141031173-chr3:141170546..141171365,3	MCF-7	breast:
18	chr3:141079682..141080290-chr3:141170633..141171265,2	K562	blood:
19	chr3:141079302..141080674-chr3:141170565..141171750,10	MCF-7	breast:
20	chr3:141169773..141172290-chr3:141203531..141206509,2	MCF-7	breast:
21	chr3:141118015..141122329-chr3:141169792..141173492,5	MCF-7	breast:
22	chr3:141082713..141089087-chr3:141169228..141173800,5	K562	blood:
23	chr3:141024124..141024878-chr3:141170738..141171518,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155893	Chromatin interaction
ENSG00000249540	Chromatin interaction
ENSG00000177311	Chromatin interaction
ENSG00000249417	Chromatin interaction
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1077181	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11707656	0.81[AMR][1000 genomes]
rs11708253	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11709875	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11714208	0.93[MEX][hapmap]
rs11716776	0.93[AMR][1000 genomes]
rs11717144	0.80[CEU][hapmap]
rs11717842	0.84[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes]
rs12695734	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12695735	0.87[CEU][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12695736	0.93[AMR][1000 genomes]
rs12695740	0.92[MEX][hapmap]
rs12695743	0.85[ASW][hapmap]
rs13072100	0.84[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13078872	0.84[CEU][hapmap];0.88[AMR][1000 genomes]
rs13083593	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes]
rs13084444	0.84[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs13088429	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13095168	0.80[CEU][hapmap]
rs13098300	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1863870	0.88[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3806647	0.81[AMR][1000 genomes]
rs720663	0.80[CEU][hapmap];0.93[MEX][hapmap]
rs7636914	0.86[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9289629	0.84[CEU][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9289634	0.80[CEU][hapmap]
rs9808953	0.80[CEU][hapmap]
rs9822575	0.80[CEU][hapmap];0.93[MEX][hapmap]
rs9830055	0.80[CEU][hapmap]
rs9833121	0.80[CEU][hapmap];0.93[MEX][hapmap]
rs9836050	0.80[CEU][hapmap]
rs9837202	0.88[CEU][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9838230	0.81[AMR][1000 genomes]
rs9849180	0.84[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes]
rs9850416	0.80[CEU][hapmap];0.93[MEX][hapmap]
rs9865971	0.83[CEU][hapmap];0.93[MEX][hapmap]
rs9868956	0.80[CEU][hapmap]
rs9870749	0.80[CEU][hapmap];0.93[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13059128	RASA2	cis	parietal	SCAN
rs13059128	RASA2	cis	cerebellum	SCAN
rs13059128	PLSCR1	cis	cerebellum	SCAN
rs13059128	GK5	cis	parietal	SCAN
rs13059128	ATP1B3	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141160400-141174000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:141162600-141171200	Weak transcription	Thymus	Thymus
3	chr3:141163000-141174000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:141163600-141171200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:141163600-141171200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:141164000-141174000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:141164200-141173600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:141164200-141176400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:141164400-141171200	Weak transcription	Primary T cells from cord blood	blood
10	chr3:141164400-141173200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:141164400-141173600	Weak transcription	Colonic Mucosa	Colon
12	chr3:141164600-141173000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:141164600-141173600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:141164800-141171200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr3:141164800-141173000	Weak transcription	Gastric	stomach
16	chr3:141164800-141173400	Weak transcription	Brain Substantia Nigra	brain
17	chr3:141164800-141174400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:141165000-141173800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:141166400-141173600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:141166600-141171200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:141166600-141171200	Weak transcription	Fetal Intestine Large	intestine
22	chr3:141166600-141171200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:141166600-141171800	Weak transcription	HSMMtube	muscle
24	chr3:141166600-141172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:141166600-141173400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:141166600-141173600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:141166600-141174200	Weak transcription	Ovary	ovary
28	chr3:141166600-141174600	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:141166600-141176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:141166600-141181600	Weak transcription	Pancreas	Pancrea
31	chr3:141166800-141173600	Weak transcription	Adipose Nuclei	Adipose
32	chr3:141166800-141173800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:141166800-141174000	Weak transcription	NHEK	skin
34	chr3:141166800-141176400	Weak transcription	HMEC	breast
35	chr3:141166800-141179200	Weak transcription	Fetal Brain Male	brain
36	chr3:141167000-141173200	Enhancers	NHLF	lung
37	chr3:141167400-141176600	Weak transcription	HSMM	muscle
38	chr3:141167600-141171400	Enhancers	A549	lung
39	chr3:141168000-141173800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:141168200-141171400	Enhancers	GM12878-XiMat	blood
41	chr3:141168200-141173200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:141168200-141173600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:141168400-141173400	Weak transcription	Lung	lung
44	chr3:141168400-141179200	Weak transcription	Fetal Heart	heart
45	chr3:141168600-141173400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:141168600-141181800	Weak transcription	Aorta	Aorta
47	chr3:141169000-141171200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:141169000-141173000	Weak transcription	NHDF-Ad	bronchial
49	chr3:141169000-141179000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:141169200-141172800	Enhancers	K562	blood

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