Variant report

Variant	rs2049503
Chromosome Location	chr3:143245928-143245929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs13079678	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324297	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325345	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17640527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140765	1.00[MKK][hapmap]
rs2165358	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28518169	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28679565	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35544617	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839599	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67623556	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6767943	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6768475	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6771449	0.91[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792226	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792609	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636473	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289665	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940636	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940637	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817782	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818142	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818164	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9819535	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828276	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs9829438	0.91[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842574	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9844522	1.00[ASW][hapmap];0.91[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844871	0.91[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849487	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857113	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857250	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859560	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863900	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864019	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869026	1.00[ASN][1000 genomes]
rs9873052	0.83[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs9873297	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs9873331	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874109	0.91[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875821	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882547	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2049503	CRCT1	trans	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143212600-143247400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:143223000-143256200	Weak transcription	Esophagus	oesophagus
3	chr3:143239200-143255200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:143241800-143251400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:143242000-143248000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr3:143243600-143247400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:143244000-143246800	Enhancers	HSMM	muscle
8	chr3:143244000-143247000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:143244200-143247800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:143244200-143249000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:143244400-143249000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr3:143244800-143247400	Enhancers	Primary B cells from peripheral blood	blood
13	chr3:143245000-143246800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:143245000-143247400	Enhancers	Primary B cells from cord blood	blood
15	chr3:143245200-143246000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:143245200-143246400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:143245200-143247400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:143245200-143247800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:143245200-143248800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:143245200-143254800	Weak transcription	NHLF	lung
21	chr3:143245200-143255600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:143245400-143246400	Enhancers	Dnd41	blood
23	chr3:143245400-143247400	Weak transcription	Aorta	Aorta
24	chr3:143245400-143247600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:143245400-143247600	Weak transcription	Osteobl	bone
26	chr3:143245400-143247800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:143245400-143255600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:143245600-143247200	Weak transcription	Fetal Lung	lung
29	chr3:143245600-143255000	Weak transcription	NHDF-Ad	bronchial
30	chr3:143245600-143255800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:143245800-143246200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:143245800-143246200	Weak transcription	Adipose Nuclei	Adipose
33	chr3:143245800-143247400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:143245800-143247400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:143245800-143247800	Weak transcription	HSMMtube	muscle
36	chr3:143245800-143254600	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links