Variant report

Variant	rs12629138
Chromosome Location	chr3:53373238-53373239
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53372908..53377239-chr3:53377354..53382827,7	K562	blood:

Variant related genes	Relation type
ENSG00000162290	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12632671	1.00[CEU][hapmap]
rs12633047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12635973	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs2884712	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs312480	0.85[CHB][hapmap]
rs41332244	1.00[CEU][hapmap]
rs6445567	1.00[JPT][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12629138	TKT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53338000-53374000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:53338200-53380200	Weak transcription	Fetal Brain Male	brain
3	chr3:53346000-53373600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:53346200-53378600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:53346600-53380600	Weak transcription	Spleen	Spleen
6	chr3:53352800-53380600	Weak transcription	Esophagus	oesophagus
7	chr3:53353000-53374600	Weak transcription	Fetal Brain Female	brain
8	chr3:53353000-53380600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:53353400-53377000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:53358200-53378800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:53358400-53380600	Weak transcription	Lung	lung
12	chr3:53358800-53376200	Weak transcription	K562	blood
13	chr3:53360000-53374000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:53360400-53376400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:53360600-53380400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:53360800-53375800	Weak transcription	Aorta	Aorta
17	chr3:53360800-53380600	Weak transcription	Gastric	stomach
18	chr3:53361400-53380200	Weak transcription	Colonic Mucosa	Colon
19	chr3:53361600-53379000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:53362600-53376200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:53362600-53376400	Weak transcription	Stomach Mucosa	stomach
22	chr3:53362800-53378200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:53362800-53380400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:53363200-53374000	Weak transcription	NHLF	lung
25	chr3:53363200-53375200	Weak transcription	Ovary	ovary
26	chr3:53363200-53376600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:53363200-53378400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:53363200-53380600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:53363400-53380400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:53363600-53378800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:53363800-53379000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:53364200-53377800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:53364400-53378600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr3:53364600-53376600	Weak transcription	Right Ventricle	heart
35	chr3:53365000-53378800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:53365200-53376400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:53365200-53376400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:53365200-53376600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:53365400-53377600	Strong transcription	Osteobl	bone
40	chr3:53365400-53378200	Strong transcription	Fetal Lung	lung
41	chr3:53365400-53378600	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr3:53365600-53377800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:53365600-53378800	Strong transcription	Placenta	Placenta
44	chr3:53365600-53379200	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:53366200-53374400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:53366200-53376600	Weak transcription	Brain Anterior Caudate	brain
47	chr3:53366200-53376800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:53366200-53379800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:53366200-53380200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:53367200-53376400	Strong transcription	HUVEC	blood vessel

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