Variant report

Variant	rs62153764
Chromosome Location	chr2:99818612-99818613
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99802213..99804900-chr2:99817713..99819435,2	K562	blood:
2	chr2:99813823..99816682-chr2:99817517..99820204,2	K562	blood:
3	chr2:99813823..99816530-chr2:99816715..99819575,3	K562	blood:

Variant related genes	Relation type
ENSG00000185414	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10198056	0.82[ASN][1000 genomes]
rs11897712	0.85[EUR][1000 genomes]
rs12053372	0.84[EUR][1000 genomes]
rs12466388	0.81[EUR][1000 genomes]
rs12474833	0.92[EUR][1000 genomes]
rs12475034	0.84[ASN][1000 genomes]
rs12477438	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17760953	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1922624	0.83[EUR][1000 genomes]
rs1968916	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3851334	0.92[EUR][1000 genomes]
rs4851196	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58206803	0.81[EUR][1000 genomes]
rs62156364	0.84[ASN][1000 genomes]
rs6542873	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73963398	0.83[EUR][1000 genomes]
rs995617	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs62153764	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs62153764	TSGA10	cis	multi-tissue	Pritchard
rs62153764	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs62153764	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs62153764	MITD1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798600-99822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
3	chr2:99798800-99825600	Weak transcription	Fetal Heart	heart
4	chr2:99799200-99824200	Weak transcription	Fetal Brain Male	brain
5	chr2:99803800-99829600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:99806000-99820000	Weak transcription	Colonic Mucosa	Colon
7	chr2:99807000-99832600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr2:99807600-99825000	Weak transcription	Stomach Mucosa	stomach
9	chr2:99812200-99819000	Weak transcription	NHDF-Ad	bronchial
10	chr2:99814000-99834800	Weak transcription	Gastric	stomach
11	chr2:99814200-99820200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:99814200-99823600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:99814200-99828200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:99814200-99832400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:99814400-99819800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:99814400-99842200	Weak transcription	Ovary	ovary
17	chr2:99814400-99842800	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:99814800-99840600	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:99815000-99823000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:99815000-99829000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:99815000-99834400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:99815000-99836400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:99815000-99840600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:99815000-99840800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:99815000-99841800	Weak transcription	Pancreas	Pancrea
26	chr2:99815000-99842400	Weak transcription	Fetal Lung	lung
27	chr2:99815200-99819400	Weak transcription	Osteobl	bone
28	chr2:99815200-99819600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:99815200-99819600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:99815200-99819800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr2:99815200-99819800	Weak transcription	NHLF	lung
32	chr2:99815200-99820000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:99815200-99821600	Weak transcription	Fetal Intestine Small	intestine
34	chr2:99815200-99821800	Weak transcription	Placenta	Placenta
35	chr2:99815200-99827400	Weak transcription	HMEC	breast
36	chr2:99815200-99827600	Weak transcription	Brain Germinal Matrix	brain
37	chr2:99815200-99827600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:99815200-99830400	Weak transcription	Brain Anterior Caudate	brain
39	chr2:99815200-99833200	Weak transcription	Lung	lung
40	chr2:99815200-99838400	Weak transcription	Adipose Nuclei	Adipose
41	chr2:99815200-99840600	Weak transcription	Aorta	Aorta
42	chr2:99815200-99841800	Weak transcription	Spleen	Spleen
43	chr2:99815200-99842000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:99815200-99842400	Weak transcription	Brain Substantia Nigra	brain
45	chr2:99815400-99819600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:99815400-99819600	Weak transcription	K562	blood
47	chr2:99815400-99820400	Weak transcription	Right Ventricle	heart
48	chr2:99815400-99820600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:99815400-99821200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:99815400-99821600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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