Variant report

Variant	rs7429596
Chromosome Location	chr3:48808531-48808532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48807713..48809774-chr3:48894172..48896397,2	K562	blood:

Variant related genes	Relation type
ENSG00000178537	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12715430	0.81[EUR][1000 genomes]
rs14018	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4974083	0.81[EUR][1000 genomes]
rs4974088	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6442131	0.91[EUR][1000 genomes]
rs6766238	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6796790	0.91[EUR][1000 genomes]
rs6801211	0.91[EUR][1000 genomes]
rs7621226	0.84[EUR][1000 genomes]
rs7639370	0.91[EUR][1000 genomes]
rs7641050	0.80[EUR][1000 genomes]
rs7653408	0.81[EUR][1000 genomes]
rs9284885	0.87[EUR][1000 genomes]
rs9311431	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9848268	0.80[EUR][1000 genomes]
rs9859473	0.90[EUR][1000 genomes]
rs9864243	0.81[EUR][1000 genomes]
rs9873227	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9879978	0.93[EUR][1000 genomes]
rs9882443	0.80[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3407876	chr3:48774454-48823998	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7429596	AMT	cis	Thyroid	GTEx
rs7429596	NICN1	cis	Thyroid	GTEx
rs7429596	NICN1-AS1	cis	Thyroid	GTEx
rs7429596	AMT	cis	Whole Blood	GTEx
rs7429596	WDR6	cis	Muscle Skeletal	GTEx
rs7429596	AMT	cis	lung	GTEx
rs7429596	P4HTM	cis	lung	GTEx
rs7429596	AMT	cis	Artery Tibial	GTEx
rs7429596	AMT	cis	Esophagus Mucosa	GTEx
rs7429596	AMT	cis	Nerve Tibial	GTEx
rs7429596	AMT	cis	Adipose Subcutaneous	GTEx
rs7429596	WDR6	cis	Nerve Tibial	GTEx
rs7429596	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs7429596	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs7429596	AMT	cis	Artery Aorta	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48778200-48814400	Weak transcription	Fetal Heart	heart
2	chr3:48778200-48820200	Weak transcription	Fetal Kidney	kidney
3	chr3:48778200-48836600	Weak transcription	A549	lung
4	chr3:48778600-48826000	Weak transcription	Stomach Mucosa	stomach
5	chr3:48782200-48814400	Weak transcription	K562	blood
6	chr3:48783400-48811400	Strong transcription	Fetal Stomach	stomach
7	chr3:48785400-48819200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:48786200-48812600	Strong transcription	Fetal Muscle Leg	muscle
9	chr3:48786600-48812800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:48789400-48844000	Weak transcription	Fetal Lung	lung
11	chr3:48789600-48820200	Weak transcription	Fetal Brain Male	brain
12	chr3:48789600-48820400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:48789600-48825800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr3:48789800-48819000	Weak transcription	Small Intestine	intestine
15	chr3:48790000-48819600	Weak transcription	NHLF	lung
16	chr3:48790200-48823600	Weak transcription	HMEC	breast
17	chr3:48791200-48825800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:48793200-48825800	Weak transcription	Fetal Thymus	thymus
19	chr3:48794600-48811800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:48794800-48810200	Weak transcription	Hela-S3	cervix
21	chr3:48794800-48819600	Weak transcription	NHDF-Ad	bronchial
22	chr3:48795200-48819600	Weak transcription	Colonic Mucosa	Colon
23	chr3:48795200-48833600	Weak transcription	Psoas Muscle	Psoas
24	chr3:48797000-48823400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:48800600-48811200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:48800800-48810600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:48801400-48811200	Strong transcription	Fetal Intestine Small	intestine
28	chr3:48802200-48832600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:48802600-48809200	Weak transcription	Placenta	Placenta
30	chr3:48802600-48819600	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:48802800-48820400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:48803800-48809400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:48805400-48812400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:48805600-48813200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:48805600-48813400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:48806200-48810400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:48806400-48812000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:48806800-48810400	Strong transcription	Primary T cells from cord blood	blood
39	chr3:48806800-48811200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:48807000-48810200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:48807000-48810600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:48807000-48810600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:48807000-48810600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr3:48807000-48812800	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr3:48807200-48809000	Strong transcription	Gastric	stomach
46	chr3:48807200-48809000	Strong transcription	Spleen	Spleen
47	chr3:48807200-48809600	Strong transcription	Ovary	ovary
48	chr3:48807200-48810000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:48807200-48810000	Strong transcription	Fetal Brain Female	brain
50	chr3:48807200-48810400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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