Variant report

Variant	rs13085205
Chromosome Location	chr3:143286592-143286593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12494880	0.80[EUR][1000 genomes]
rs13061398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13064748	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13068070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13069703	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13071089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13074668	0.87[EUR][1000 genomes]
rs13074737	0.86[EUR][1000 genomes]
rs13076949	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13090915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1405017	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1525858	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1525862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525863	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16853857	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17640925	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1983467	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35417581	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35593863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4839601	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4839602	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4839642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71307941	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71307942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs746055	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7642430	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][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	nsv829745	chr3:143278512-143405626	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143256000-143305600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:143270600-143304800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:143277400-143292400	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:143277400-143301200	Weak transcription	Esophagus	oesophagus
5	chr3:143277400-143303600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:143277400-143310200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr3:143277600-143292400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:143279000-143296200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:143281400-143292200	Weak transcription	Primary T cells from cord blood	blood
10	chr3:143284000-143287200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:143284000-143306400	Weak transcription	Spleen	Spleen
12	chr3:143284400-143287400	Enhancers	Fetal Intestine Small	intestine
13	chr3:143284400-143292600	Weak transcription	Brain Substantia Nigra	brain
14	chr3:143284400-143299200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr3:143284600-143286800	Enhancers	Primary B cells from peripheral blood	blood
16	chr3:143284600-143287000	Enhancers	Fetal Intestine Large	intestine
17	chr3:143285000-143300400	Weak transcription	Brain Anterior Caudate	brain
18	chr3:143285200-143290400	Weak transcription	Adipose Nuclei	Adipose
19	chr3:143285200-143290400	Weak transcription	Fetal Lung	lung
20	chr3:143285200-143290600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:143285200-143292200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:143285400-143286600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:143285400-143286600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:143285400-143290800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:143285600-143296200	Weak transcription	Primary B cells from cord blood	blood
26	chr3:143285800-143287400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:143286200-143286800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:143286200-143287600	Enhancers	HUVEC	blood vessel
29	chr3:143286200-143290400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr3:143286200-143290600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:143286400-143286800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr3:143286400-143286800	Enhancers	GM12878-XiMat	blood
33	chr3:143286400-143287000	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr3:143286400-143287200	Enhancers	Brain Germinal Matrix	brain
35	chr3:143286400-143287200	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links