Variant report

Variant	rs2293251
Chromosome Location	chr3:138124114-138124115
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:109618765..109621666-chr3:138122913..138124560,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10513053	0.89[JPT][hapmap]
rs1199337	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1199338	1.00[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs12695685	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074317	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13079209	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13080413	1.00[ASN][1000 genomes]
rs13083299	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096934	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324341	0.93[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs1720819	0.86[GIH][hapmap]
rs185244	0.83[EUR][1000 genomes]
rs2279241	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291127	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347252	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34078858	0.84[ASN][1000 genomes]
rs34140440	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34568901	1.00[ASN][1000 genomes]
rs34905952	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3732837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773750	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs59217491	0.84[ASN][1000 genomes]
rs6807945	0.93[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs9818870	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828345	1.00[JPT][hapmap]
rs9848655	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851766	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864898	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872754	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1845560	chr3:138087467-138133412	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2293251	MRAS	cis	Artery Aorta	GTEx
rs2293251	RBP1	cis	parietal	SCAN
rs2293251	TRIM42	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138109600-138124400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:138109800-138124800	Weak transcription	NHLF	lung
3	chr3:138109800-138131400	Weak transcription	NHDF-Ad	bronchial
4	chr3:138114000-138126200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:138114800-138124600	Strong transcription	Fetal Stomach	stomach
6	chr3:138115800-138125200	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:138116000-138124600	Strong transcription	Aorta	Aorta
8	chr3:138116000-138125200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:138116000-138125200	Strong transcription	HSMM	muscle
10	chr3:138116000-138125800	Strong transcription	Fetal Brain Female	brain
11	chr3:138116000-138127000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:138116200-138125000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:138116200-138125800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:138116200-138126200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:138116400-138125200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:138116600-138125200	Strong transcription	Brain Germinal Matrix	brain
17	chr3:138116800-138124600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr3:138117000-138125200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr3:138117200-138124600	Strong transcription	Adipose Nuclei	Adipose
20	chr3:138117200-138124600	Strong transcription	Lung	lung
21	chr3:138117200-138124800	Strong transcription	Osteobl	bone
22	chr3:138117200-138125000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:138117400-138126800	Weak transcription	Fetal Brain Male	brain
24	chr3:138118000-138127000	Weak transcription	Fetal Kidney	kidney
25	chr3:138118000-138131800	Weak transcription	Right Atrium	heart
26	chr3:138118400-138124600	Weak transcription	Fetal Intestine Small	intestine
27	chr3:138118400-138124800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:138118800-138124200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:138118800-138125200	Strong transcription	Brain Cingulate Gyrus	brain
30	chr3:138119400-138124400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr3:138119400-138127000	Weak transcription	Psoas Muscle	Psoas
32	chr3:138119600-138124800	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:138119600-138125000	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:138120000-138124800	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:138120200-138124800	Strong transcription	Left Ventricle	heart
36	chr3:138120200-138124800	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:138120200-138125000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr3:138120200-138125200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr3:138120200-138126800	Weak transcription	HepG2	liver
40	chr3:138120600-138124800	Strong transcription	Brain Anterior Caudate	brain
41	chr3:138121200-138124800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:138121200-138125200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr3:138121200-138125600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:138121200-138126400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:138121200-138126400	Strong transcription	HSMMtube	muscle
46	chr3:138121400-138124800	Strong transcription	Right Ventricle	heart
47	chr3:138121400-138127000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:138121800-138126600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr3:138122200-138126800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:138122400-138124600	Strong transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links