Variant report

Variant	rs56972966
Chromosome Location	chr3:53212179-53212180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53206928..53209011-chr3:53211960..53213627,2	K562	blood:
2	chr3:53206286..53208790-chr3:53209926..53212875,3	K562	blood:
3	chr3:53162337..53164765-chr3:53211790..53213613,2	MCF-7	breast:
4	chr3:53193644..53196827-chr3:53209884..53213344,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163933	Chromatin interaction
ENSG00000163932	Chromatin interaction

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

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

rs_ID	r²[population]
rs13319192	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035451	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59254509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967449	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750527	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750528	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862206	0.83[AMR][1000 genomes];0.86[EUR][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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56972966	TKT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53196400-53212400	Weak transcription	Aorta	Aorta
2	chr3:53197200-53213400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:53197600-53227600	Weak transcription	Hela-S3	cervix
4	chr3:53197800-53214000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:53198000-53215600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:53200600-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:53201400-53212400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:53201400-53212600	Weak transcription	Ovary	ovary
9	chr3:53201400-53212800	Weak transcription	Left Ventricle	heart
10	chr3:53201600-53212800	Weak transcription	NHDF-Ad	bronchial
11	chr3:53201600-53228000	Weak transcription	NH-A	brain
12	chr3:53202000-53212400	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:53202000-53212600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:53202000-53228400	Weak transcription	Fetal Kidney	kidney
15	chr3:53202800-53229600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:53203200-53226800	Strong transcription	Fetal Stomach	stomach
17	chr3:53203600-53212800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:53203600-53229800	Weak transcription	A549	lung
19	chr3:53204000-53212600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:53204600-53213600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:53205600-53229800	Weak transcription	Brain Angular Gyrus	brain
22	chr3:53205800-53213800	Weak transcription	Small Intestine	intestine
23	chr3:53206000-53212400	Weak transcription	Fetal Lung	lung
24	chr3:53206000-53212600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:53206000-53213600	Weak transcription	Brain Substantia Nigra	brain
26	chr3:53206000-53213800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:53206000-53219400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:53206400-53212400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:53206400-53216600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:53206400-53217000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:53206600-53212400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:53206600-53212600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:53206600-53212800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:53206600-53213200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:53206600-53215400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:53206600-53221400	Strong transcription	Fetal Intestine Small	intestine
37	chr3:53206800-53213200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:53206800-53215600	Genic enhancers	Primary monocytes fromperipheralblood	blood
39	chr3:53206800-53219400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr3:53206800-53228000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:53207000-53212800	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:53207000-53213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:53207000-53214200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:53207200-53213200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:53207200-53213200	Genic enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:53207200-53227400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:53207200-53227600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:53207400-53212600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:53208000-53212600	Weak transcription	Primary T cells from cord blood	blood
50	chr3:53208200-53212400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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