Variant report

Variant	rs17023045
Chromosome Location	chr2:38916474-38916475
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38914282..38916559-chr2:38977085..38978615,2	MCF-7	breast:
2	chr2:38828223..38831586-chr2:38916427..38918985,3	MCF-7	breast:
3	chr2:38895714..38897624-chr2:38914031..38916538,2	K562	blood:
4	chr2:38915899..38920812-chr2:38977039..38979793,4	K562	blood:
5	chr2:38827954..38830677-chr2:38913858..38916720,4	K562	blood:
6	chr2:38914950..38917916-chr2:38919871..38923223,3	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000143889	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10165289	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10180775	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10186448	1.00[CEU][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10194503	0.95[AFR][1000 genomes]
rs12712612	0.83[YRI][hapmap]
rs13382974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13396461	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13399254	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13409776	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13420732	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13421894	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17023037	1.00[EUR][1000 genomes]
rs17023042	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17425982	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2218850	1.00[EUR][1000 genomes]
rs2373466	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2373472	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs28473018	1.00[EUR][1000 genomes]
rs28499207	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28716236	0.81[AFR][1000 genomes]
rs3099938	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099947	1.00[CEU][hapmap]
rs3099973	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3099986	1.00[EUR][1000 genomes]
rs3099996	1.00[EUR][1000 genomes]
rs3099997	1.00[EUR][1000 genomes]
rs3112145	1.00[EUR][1000 genomes]
rs3112146	1.00[EUR][1000 genomes]
rs3112148	1.00[EUR][1000 genomes]
rs3112155	1.00[EUR][1000 genomes]
rs3112157	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112158	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112160	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112164	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3112174	1.00[EUR][1000 genomes]
rs62142714	1.00[AMR][1000 genomes]
rs6752602	0.88[AFR][1000 genomes]
rs7564672	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17023045	MAP4K3	cis	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894000-38917600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr2:38894200-38919000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:38894400-38917600	Weak transcription	NHDF-Ad	bronchial
4	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:38894600-38919600	Weak transcription	Fetal Heart	heart
6	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:38895000-38917600	Weak transcription	HSMM	muscle
8	chr2:38898600-38921200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:38901400-38917000	Weak transcription	HSMMtube	muscle
10	chr2:38902800-38916600	Strong transcription	Fetal Stomach	stomach
11	chr2:38903600-38923800	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:38903800-38918600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:38904400-38918400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:38905000-38917000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:38905000-38917800	Weak transcription	Esophagus	oesophagus
17	chr2:38905000-38918400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:38905000-38935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:38905200-38920400	Strong transcription	Fetal Intestine Large	intestine
21	chr2:38905200-38925400	Weak transcription	Small Intestine	intestine
22	chr2:38905600-38917600	Strong transcription	Fetal Intestine Small	intestine
23	chr2:38906400-38918800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr2:38908800-38917600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:38909000-38918000	Weak transcription	Colonic Mucosa	Colon
26	chr2:38909200-38917600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:38909200-38917600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:38909200-38917800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:38909200-38921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:38909200-38947800	Weak transcription	Right Ventricle	heart
31	chr2:38909400-38921200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:38909400-38921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:38909600-38947800	Weak transcription	Brain Anterior Caudate	brain
35	chr2:38909800-38938600	Weak transcription	Fetal Kidney	kidney
36	chr2:38910000-38948000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:38910400-38917600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:38911000-38919000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:38911600-38920600	Strong transcription	Thymus	Thymus
40	chr2:38911800-38916600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:38912400-38917000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:38912400-38917600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:38912600-38920800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:38912600-38921000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:38912600-38932000	Weak transcription	Colon Smooth Muscle	Colon
46	chr2:38912800-38916600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:38912800-38917400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr2:38912800-38917600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:38912800-38917600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:38912800-38917600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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