Variant report

Variant	rs12492129
Chromosome Location	chr3:53351887-53351888
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11915147	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11919567	0.96[ASN][1000 genomes]
rs12487816	1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs12488901	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12491594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12496449	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12496915	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2128710	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs41332244	1.00[CHD][hapmap];0.91[GIH][hapmap]
rs73843118	1.00[AMR][1000 genomes];1.00[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	nsv876801	chr3:53325905-53467506	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv876802	chr3:53325905-53470863	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53322400-53353600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:53326600-53364400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:53327200-53358200	Weak transcription	K562	blood
4	chr3:53332600-53355600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:53334600-53355200	Strong transcription	Fetal Stomach	stomach
6	chr3:53334600-53358400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:53335400-53354200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr3:53338000-53374000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:53338200-53352000	Weak transcription	Colonic Mucosa	Colon
10	chr3:53338200-53352600	Weak transcription	A549	lung
11	chr3:53338200-53355200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:53338200-53380200	Weak transcription	Fetal Brain Male	brain
13	chr3:53338400-53367400	Weak transcription	Small Intestine	intestine
14	chr3:53341000-53353200	Strong transcription	Primary T cells from cord blood	blood
15	chr3:53341200-53353200	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:53341200-53354800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:53342600-53354000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr3:53344000-53354400	Weak transcription	Psoas Muscle	Psoas
19	chr3:53344000-53364200	Weak transcription	Right Ventricle	heart
20	chr3:53344600-53355600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:53344600-53358200	Weak transcription	Pancreas	Pancrea
22	chr3:53345600-53352000	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:53345800-53357800	Strong transcription	Fetal Intestine Small	intestine
24	chr3:53345800-53362600	Weak transcription	NHLF	lung
25	chr3:53346000-53352600	Weak transcription	HSMM	muscle
26	chr3:53346000-53373600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr3:53346200-53352800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:53346200-53365200	Weak transcription	Fetal Kidney	kidney
29	chr3:53346200-53378600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:53346400-53352000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:53346400-53352000	Weak transcription	Esophagus	oesophagus
32	chr3:53346400-53352600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:53346400-53352800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:53346400-53354800	Weak transcription	Brain Substantia Nigra	brain
35	chr3:53346400-53358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:53346400-53358200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:53346400-53358200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:53346400-53360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:53346400-53360400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:53346400-53360400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:53346400-53360400	Weak transcription	Aorta	Aorta
42	chr3:53346400-53360400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:53346400-53362200	Weak transcription	Stomach Mucosa	stomach
44	chr3:53346400-53362800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:53346400-53365400	Weak transcription	Brain Angular Gyrus	brain
46	chr3:53346400-53367600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr3:53346400-53370000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:53346600-53352600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:53346600-53380600	Weak transcription	Spleen	Spleen
50	chr3:53347000-53352400	Weak transcription	NH-A	brain

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