Variant report

Variant	rs12488901
Chromosome Location	chr3:53352476-53352477
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11915147	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11919567	0.96[ASN][1000 genomes]
rs12487816	1.00[AMR][1000 genomes]
rs12491594	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12492129	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12494167	0.81[AMR][1000 genomes]
rs12496449	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12496915	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12631120	0.81[AMR][1000 genomes]
rs1961499	0.81[AMR][1000 genomes]
rs2128710	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73843118	0.86[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	chr3:53338200-53352600	Weak transcription	A549	lung
10	chr3:53338200-53355200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:53338200-53380200	Weak transcription	Fetal Brain Male	brain
12	chr3:53338400-53367400	Weak transcription	Small Intestine	intestine
13	chr3:53341000-53353200	Strong transcription	Primary T cells from cord blood	blood
14	chr3:53341200-53353200	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:53341200-53354800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:53342600-53354000	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:53344000-53354400	Weak transcription	Psoas Muscle	Psoas
18	chr3:53344000-53364200	Weak transcription	Right Ventricle	heart
19	chr3:53344600-53355600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:53344600-53358200	Weak transcription	Pancreas	Pancrea
21	chr3:53345800-53357800	Strong transcription	Fetal Intestine Small	intestine
22	chr3:53345800-53362600	Weak transcription	NHLF	lung
23	chr3:53346000-53352600	Weak transcription	HSMM	muscle
24	chr3:53346000-53373600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:53346200-53352800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:53346200-53365200	Weak transcription	Fetal Kidney	kidney
27	chr3:53346200-53378600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:53346400-53352600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:53346400-53352800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:53346400-53354800	Weak transcription	Brain Substantia Nigra	brain
31	chr3:53346400-53358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr3:53346400-53358200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:53346400-53358200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:53346400-53360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:53346400-53360400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr3:53346400-53360400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:53346400-53360400	Weak transcription	Aorta	Aorta
38	chr3:53346400-53360400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:53346400-53362200	Weak transcription	Stomach Mucosa	stomach
40	chr3:53346400-53362800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:53346400-53365400	Weak transcription	Brain Angular Gyrus	brain
42	chr3:53346400-53367600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr3:53346400-53370000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:53346600-53352600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:53346600-53380600	Weak transcription	Spleen	Spleen
46	chr3:53347000-53352800	Weak transcription	Brain Anterior Caudate	brain
47	chr3:53347000-53357200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr3:53347000-53359200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr3:53347200-53360400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr3:53347200-53371400	Weak transcription	HMEC	breast

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