Variant report

Variant	rs12469458
Chromosome Location	chr2:38911819-38911820
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38908524..38910141-chr2:38911332..38912843,2	MCF-7	breast:
2	chr2:38906476..38910309-chr2:38910692..38914128,4	K562	blood:
3	chr2:38907772..38911113-chr2:38911732..38914917,4	K562	blood:
4	chr2:38909532..38914838-chr2:38917160..38922190,4	K562	blood:
5	chr2:38903554..38905525-chr2:38909598..38912564,2	MCF-7	breast:
6	chr2:38910654..38912179-chr2:38977560..38979833,2	K562	blood:

Variant related genes	Relation type
ENSG00000143891	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10203706	0.86[AFR][1000 genomes]
rs12469534	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12712612	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13004674	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13004806	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13004842	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13005073	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13006376	0.97[EUR][1000 genomes]
rs13010022	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13012704	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13016907	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13032255	0.82[ASN][1000 genomes]
rs13383762	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17576472	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17576507	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28716236	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34391548	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34533539	0.91[ASN][1000 genomes]
rs34558770	0.88[EUR][1000 genomes]
rs34756536	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34875979	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34909144	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35448554	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35585199	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4670885	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58757994	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6707543	0.82[ASN][1000 genomes]
rs6736380	0.82[ASN][1000 genomes]
rs6741892	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][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
rs12469458	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 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	chr2:38895600-38912400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:38898600-38912400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:38898600-38921200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:38901400-38917000	Weak transcription	HSMMtube	muscle
12	chr2:38902800-38916600	Strong transcription	Fetal Stomach	stomach
13	chr2:38903000-38912200	Strong transcription	Fetal Muscle Leg	muscle
14	chr2:38903000-38912400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:38903000-38912800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:38903200-38912800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:38903600-38923800	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:38903800-38918600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr2:38904400-38918400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:38905000-38913600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:38905000-38917000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:38905000-38917800	Weak transcription	Esophagus	oesophagus
24	chr2:38905000-38918400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:38905000-38935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:38905200-38912400	Weak transcription	Stomach Mucosa	stomach
28	chr2:38905200-38912400	Weak transcription	NHLF	lung
29	chr2:38905200-38912600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:38905200-38915400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:38905200-38920400	Strong transcription	Fetal Intestine Large	intestine
32	chr2:38905200-38925400	Weak transcription	Small Intestine	intestine
33	chr2:38905600-38917600	Strong transcription	Fetal Intestine Small	intestine
34	chr2:38906400-38918800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr2:38907800-38912200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:38908800-38912200	Weak transcription	Ovary	ovary
37	chr2:38908800-38917600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:38909000-38912400	Weak transcription	Gastric	stomach
39	chr2:38909000-38918000	Weak transcription	Colonic Mucosa	Colon
40	chr2:38909200-38912000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:38909200-38912400	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:38909200-38913800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:38909200-38913800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr2:38909200-38913800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:38909200-38914000	Weak transcription	Aorta	Aorta
46	chr2:38909200-38914000	Weak transcription	Spleen	Spleen
47	chr2:38909200-38917600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:38909200-38917600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:38909200-38917800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:38909200-38921200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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