Variant report

Variant	rs17023042
Chromosome Location	chr2:38912786-38912787
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38827976..38829875-chr2:38912577..38914766,2	MCF-7	breast:
2	chr2:38908524..38910141-chr2:38911332..38912843,2	MCF-7	breast:
3	chr2:38906476..38910309-chr2:38910692..38914128,4	K562	blood:
4	chr2:38824210..38826669-chr2:38912161..38913673,2	MCF-7	breast:
5	chr2:38907772..38911113-chr2:38911732..38914917,4	K562	blood:
6	chr2:38909532..38914838-chr2:38917160..38922190,4	K562	blood:

Variant related genes	Relation type
ENSG00000143891	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000235586	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10165289	1.00[CEU][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10180775	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10186448	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12712612	0.84[ASW][hapmap];0.91[LWK][hapmap];0.91[YRI][hapmap]
rs13010022	0.91[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs13382974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13396461	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13399254	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13409776	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13420732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13421894	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17023037	1.00[EUR][1000 genomes]
rs17023045	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]
rs17576507	0.91[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][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	1.00[AMR][1000 genomes];1.00[EUR][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]
rs34756536	0.84[AFR][1000 genomes]
rs4670885	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs62142714	1.00[AMR][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

No data

Chromatin state (count:105 , 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	chr2:38903000-38912800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:38903200-38912800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:38903600-38923800	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:38903800-38918600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:38904400-38918400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:38905000-38913600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:38905000-38917000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:38905000-38917800	Weak transcription	Esophagus	oesophagus
20	chr2:38905000-38918400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:38905000-38935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:38905200-38915400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:38905200-38920400	Strong transcription	Fetal Intestine Large	intestine
25	chr2:38905200-38925400	Weak transcription	Small Intestine	intestine
26	chr2:38905600-38917600	Strong transcription	Fetal Intestine Small	intestine
27	chr2:38906400-38918800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr2:38908800-38917600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:38909000-38918000	Weak transcription	Colonic Mucosa	Colon
30	chr2:38909200-38913800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:38909200-38913800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:38909200-38913800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:38909200-38914000	Weak transcription	Aorta	Aorta
34	chr2:38909200-38914000	Weak transcription	Spleen	Spleen
35	chr2:38909200-38917600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:38909200-38917600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:38909200-38917800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:38909200-38921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:38909200-38947800	Weak transcription	Right Ventricle	heart
40	chr2:38909400-38913800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:38909400-38913800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:38909400-38915200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:38909400-38916200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr2:38909400-38921200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:38909400-38921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:38909600-38913800	Weak transcription	Fetal Lung	lung
48	chr2:38909600-38947800	Weak transcription	Brain Anterior Caudate	brain
49	chr2:38909800-38913800	Weak transcription	Fetal Muscle Trunk	muscle
50	chr2:38909800-38938600	Weak transcription	Fetal Kidney	kidney

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