Variant report

Variant	rs4955440
Chromosome Location	chr3:49388633-49388634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:49387116..49389894-chr3:49449590..49451097,2	K562	blood:
2	chr3:49385803..49389031-chr3:49447399..49451143,5	K562	blood:
3	chr3:49388313..49390760-chr3:49397473..49400161,2	K562	blood:
4	chr3:49376089..49379418-chr3:49384584..49389123,6	K562	blood:
5	chr3:49387350..49389031-chr3:49446931..49448922,3	K562	blood:

Variant related genes	Relation type
ENSG00000114316	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4955413	0.80[AMR][1000 genomes]
rs4955424	0.81[EUR][1000 genomes]
rs4955425	0.80[EUR][1000 genomes]

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs4955440	AMT	cis	lung	GTEx
rs4955440	AMT	cis	Artery Aorta	GTEx
rs4955440	AMT	cis	Adipose Subcutaneous	GTEx
rs4955440	AMT	cis	Esophagus Muscularis	GTEx
rs4955440	AMT	Cis_1M	lymphoblastoid	RTeQTL
rs4955440	AMT	cis	Nerve Tibial	GTEx
rs4955440	NICN1-AS1	cis	Thyroid	GTEx
rs4955440	AMT,NICN1	cis	brain	BrainEAC
rs4955440	AMT	cis	Artery Tibial	GTEx
rs4955440	NICN1	cis	Thyroid	GTEx
rs4955440	WDR6	cis	Nerve Tibial	GTEx
rs4955440	AMT	cis	Whole Blood	GTEx
rs4955440	AMT	cis	Thyroid	GTEx
rs4955440	AMT	cis	Esophagus Mucosa	GTEx
rs4955440	AMT	cis	Skin Sun Exposed Lower leg	GTEx
rs4955440	WDR6	cis	Muscle Skeletal	GTEx
rs4955440	AMT	cis	Muscle Skeletal	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49378600-49388800	Weak transcription	Brain Substantia Nigra	brain
2	chr3:49378600-49388800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:49378600-49390000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:49378600-49392000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:49379000-49392000	Weak transcription	Left Ventricle	heart
6	chr3:49379800-49392800	Weak transcription	Thymus	Thymus
7	chr3:49381400-49388800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:49381600-49393000	Weak transcription	Right Atrium	heart
9	chr3:49383000-49388800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:49383000-49388800	Weak transcription	Fetal Thymus	thymus
11	chr3:49383000-49389200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:49383000-49389400	Weak transcription	Spleen	Spleen
13	chr3:49383000-49393600	Weak transcription	Primary T cells from cord blood	blood
14	chr3:49383200-49391800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:49383200-49392400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr3:49383400-49389000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:49383400-49391400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr3:49384600-49388800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:49384600-49388800	Weak transcription	HSMMtube	muscle
20	chr3:49384600-49389000	Weak transcription	NH-A	brain
21	chr3:49384600-49392000	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:49384600-49392400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:49384800-49388800	Weak transcription	Psoas Muscle	Psoas
24	chr3:49384800-49391800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:49385200-49388800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:49385200-49388800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:49385200-49389000	Enhancers	Hela-S3	cervix
28	chr3:49385800-49389600	Enhancers	Fetal Intestine Small	intestine
29	chr3:49385800-49390200	Enhancers	Fetal Intestine Large	intestine
30	chr3:49386200-49389000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:49386400-49390200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr3:49386400-49390800	Enhancers	Primary hematopoietic stem cells	blood
33	chr3:49386400-49390800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:49386400-49390800	Enhancers	Adipose Nuclei	Adipose
35	chr3:49386400-49390800	Enhancers	K562	blood
36	chr3:49386800-49390400	Enhancers	Placenta	Placenta
37	chr3:49387000-49389200	Weak transcription	Fetal Kidney	kidney
38	chr3:49387000-49393000	Weak transcription	Aorta	Aorta
39	chr3:49387200-49389800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:49387200-49391400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:49387200-49392800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:49387400-49388800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:49387400-49388800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:49387400-49389200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:49387400-49392800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:49387400-49393000	Weak transcription	Right Ventricle	heart
47	chr3:49387400-49393800	Weak transcription	Gastric	stomach
48	chr3:49387600-49388800	Weak transcription	Stomach Mucosa	stomach
49	chr3:49387600-49389000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:49387600-49390800	Enhancers	Primary B cells from cord blood	blood

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