Variant report

Variant	rs58757994
Chromosome Location	chr2:38910869-38910870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38819202..38822030-chr2:38909046..38911240,2	K562	blood:
2	chr2:38906476..38910309-chr2:38910692..38914128,4	K562	blood:
3	chr2:38823851..38826080-chr2:38908814..38911340,2	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
ENSG00000152147	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12469458	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12469534	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12478924	0.83[ASN][1000 genomes]
rs12712612	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13004674	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13004806	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13004842	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13005073	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13006376	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs13010022	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13011383	0.93[ASN][1000 genomes]
rs13012704	0.93[EUR][1000 genomes]
rs13016907	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13029674	0.84[ASN][1000 genomes]
rs13032255	0.95[ASN][1000 genomes]
rs13383762	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13425086	0.89[ASN][1000 genomes]
rs17576472	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17576507	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373424	0.83[ASN][1000 genomes]
rs28716236	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34391548	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34533539	0.83[ASN][1000 genomes]
rs34558770	0.90[EUR][1000 genomes]
rs34756536	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34875979	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34909144	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35448554	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35585199	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4670885	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707543	0.95[ASN][1000 genomes]
rs6736380	0.95[ASN][1000 genomes]
rs6741892	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[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
rs58757994	SOS1	Cis_1M	lymphoblastoid	RTeQTL

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	chr2:38895600-38912400	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	chr2:38898800-38911600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:38901400-38917000	Weak transcription	HSMMtube	muscle
13	chr2:38902800-38916600	Strong transcription	Fetal Stomach	stomach
14	chr2:38903000-38912200	Strong transcription	Fetal Muscle Leg	muscle
15	chr2:38903000-38912400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:38903000-38912800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:38903200-38912800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr2:38903600-38923800	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:38903800-38918600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:38904400-38918400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:38904800-38936000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:38905000-38911000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr2:38905000-38911800	Weak transcription	Hela-S3	cervix
24	chr2:38905000-38913600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:38905000-38917000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:38905000-38917800	Weak transcription	Esophagus	oesophagus
27	chr2:38905000-38918400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:38905000-38935800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:38905200-38912400	Weak transcription	Stomach Mucosa	stomach
31	chr2:38905200-38912400	Weak transcription	NHLF	lung
32	chr2:38905200-38912600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:38905200-38915400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:38905200-38920400	Strong transcription	Fetal Intestine Large	intestine
35	chr2:38905200-38925400	Weak transcription	Small Intestine	intestine
36	chr2:38905600-38911200	Strong transcription	Liver	Liver
37	chr2:38905600-38911400	Strong transcription	HepG2	liver
38	chr2:38905600-38917600	Strong transcription	Fetal Intestine Small	intestine
39	chr2:38906000-38911800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:38906400-38918800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:38907800-38912200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:38908800-38912200	Weak transcription	Ovary	ovary
43	chr2:38908800-38917600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:38909000-38912400	Weak transcription	Gastric	stomach
45	chr2:38909000-38918000	Weak transcription	Colonic Mucosa	Colon
46	chr2:38909200-38911000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr2:38909200-38912000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:38909200-38912400	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:38909200-38913800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:38909200-38913800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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