Variant report

Variant	rs13404493
Chromosome Location	chr2:33756520-33756521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr2:33754903-33756949	GM12878	blood:	n/a	chr2:33756092-33756101 chr2:33756092-33756101
2	STAT3	chr2:33755779-33756566	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:33756130-33757250	GM12891	blood:	n/a	n/a
4	POLR2A	chr2:33754749-33757259	GM12892	blood:	n/a	n/a
5	RELA	chr2:33755054-33756943	GM19099	blood:	n/a	chr2:33756092-33756101 chr2:33756092-33756101
6	NFIC	chr2:33755314-33756614	GM12878	blood:	n/a	n/a
7	NFIC	chr2:33754935-33756897	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:33754839-33757394	GM12892	blood:	n/a	n/a
9	RELA	chr2:33755693-33757188	GM18951	blood:	n/a	chr2:33756092-33756101 chr2:33756092-33756101
10	PML	chr2:33754667-33756870	GM12878	blood:	n/a	chr2:33754990-33754999
11	EBF1	chr2:33756399-33756899	GM12878	blood:	n/a	n/a
12	ATF2	chr2:33754699-33757003	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:33755185-33757013	GM12892	blood:	n/a	n/a
14	MTA3	chr2:33754602-33757187	GM12878	blood:	n/a	n/a
15	RELA	chr2:33754725-33757187	GM10847	blood:	n/a	chr2:33756092-33756101 chr2:33756092-33756101
16	POLR2A	chr2:33756334-33757030	GM12892	blood:	n/a	n/a
17	FOXM1	chr2:33754756-33756580	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:33756255-33757333	GM12878	blood:	n/a	n/a
19	RCOR1	chr2:33755659-33756891	GM12878	blood:	n/a	n/a
20	WRNIP1	chr2:33756334-33756948	GM12878	blood:	n/a	n/a
21	SPI1	chr2:33756256-33756601	GM12891	blood:	n/a	chr2:33756473-33756480 chr2:33756470-33756483
22	EP300	chr2:33754788-33756655	GM12878	blood:	n/a	chr2:33755595-33755609 chr2:33756471-33756485 chr2:33755745-33755759 chr2:33754988-33754997 chr2:33756132-33756146
23	SPI1	chr2:33756280-33756592	GM12878	blood:	n/a	chr2:33756473-33756480 chr2:33756470-33756483
24	FOXM1	chr2:33755672-33756851	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:33756399-33757081	GM12891	blood:	n/a	n/a
26	RELA	chr2:33755637-33756875	GM19193	blood:	n/a	chr2:33756092-33756101 chr2:33756092-33756101
27	POLR2A	chr2:33756378-33757015	GM12891	blood:	n/a	n/a
28	STAT5A	chr2:33754755-33756621	GM12878	blood:	n/a	chr2:33754989-33754998
29	BHLHE40	chr2:33755930-33756682	GM12878	blood:	n/a	n/a
30	ZNF143	chr2:33756509-33756890	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:33754627-33756925	GM19099	blood:	n/a	n/a
32	RCOR1	chr2:33756267-33757732	IMR90	lung:	n/a	n/a
33	POLR2A	chr2:33754583-33757284	GM12878	blood:	n/a	n/a
34	ATF2	chr2:33755534-33756945	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:33754583-33757763	GM12891	blood:	n/a	n/a
36	POLR2A	chr2:33754943-33757426	GM12878	blood:	n/a	n/a
37	MTA3	chr2:33754603-33756718	GM12878	blood:	n/a	n/a
38	RELA	chr2:33755835-33757099	GM15510	blood:	n/a	chr2:33756092-33756101 chr2:33756092-33756101
39	POLR2A	chr2:33754793-33757255	GM12892	blood:	n/a	n/a
40	POLR2A	chr2:33754859-33757539	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:33756377-33757137	GM12891	blood:	n/a	n/a
42	POLR2A	chr2:33753413-33757052	Raji	blood:	n/a	n/a
43	RELA	chr2:33754673-33756965	GM18505	blood:	n/a	chr2:33756092-33756101 chr2:33756092-33756101
44	POLR2A	chr2:33754713-33757616	GM18505	blood:	n/a	n/a
45	SPI1	chr2:33756313-33756669	GM12891	blood:	n/a	chr2:33756473-33756480 chr2:33756470-33756483
46	NFATC1	chr2:33755819-33757206	GM12878	blood:	n/a	n/a
47	BCLAF1	chr2:33756280-33757386	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RASGRP3	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10186362	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11884210	0.87[EUR][1000 genomes]
rs12467474	0.87[EUR][1000 genomes]
rs12468045	0.87[EUR][1000 genomes]
rs12470399	0.89[EUR][1000 genomes]
rs12476217	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12476533	0.85[EUR][1000 genomes]
rs12478596	0.89[EUR][1000 genomes]
rs12478742	0.89[EUR][1000 genomes]
rs17013237	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17013312	0.87[EUR][1000 genomes]
rs4491711	0.87[EUR][1000 genomes]
rs4491712	0.87[EUR][1000 genomes]
rs55834207	0.89[EUR][1000 genomes]
rs57542130	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7574183	0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13404493	RASGRP3	cis	Thyroid	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33710400-33775400	Weak transcription	Pancreas	Pancrea
2	chr2:33735400-33761800	Weak transcription	Spleen	Spleen
3	chr2:33737600-33760800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:33738600-33782800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:33738800-33777200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:33739200-33761800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:33740800-33790000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:33744800-33758200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:33747200-33757600	Weak transcription	Psoas Muscle	Psoas
10	chr2:33747400-33761800	Weak transcription	Aorta	Aorta
11	chr2:33747800-33756600	Weak transcription	Right Ventricle	heart
12	chr2:33747800-33780200	Weak transcription	Brain Anterior Caudate	brain
13	chr2:33748000-33761800	Weak transcription	Fetal Stomach	stomach
14	chr2:33748000-33774400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:33748000-33790400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:33748200-33780200	Weak transcription	Brain Angular Gyrus	brain
17	chr2:33752800-33757800	Enhancers	NHDF-Ad	bronchial
18	chr2:33753000-33757000	Weak transcription	Lung	lung
19	chr2:33753000-33760600	Weak transcription	Adipose Nuclei	Adipose
20	chr2:33753400-33757800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:33754200-33758000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:33754200-33760400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:33754200-33761800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:33754600-33757200	Enhancers	HSMMtube	muscle
25	chr2:33754600-33757200	Enhancers	Osteobl	bone
26	chr2:33754600-33757800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:33754600-33757800	Enhancers	NHLF	lung
28	chr2:33754600-33758400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:33754800-33756600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:33754800-33757200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:33754800-33757400	Enhancers	HSMM	muscle
32	chr2:33755000-33758000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:33755000-33779800	Weak transcription	Small Intestine	intestine
34	chr2:33755200-33756600	Flanking Active TSS	GM12878-XiMat	blood
35	chr2:33755200-33756800	Weak transcription	Fetal Heart	heart
36	chr2:33755200-33762800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:33755200-33767800	Weak transcription	Liver	Liver
38	chr2:33755400-33757400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr2:33755400-33779800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:33755600-33756600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:33755600-33757000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:33755800-33756800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:33756200-33756600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:33756200-33759000	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr2:33756400-33757000	Genic enhancers	Primary B cells from cord blood	blood
46	chr2:33756400-33757000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:33756400-33757000	Strong transcription	Brain Hippocampus Middle	brain
48	chr2:33756400-33757200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:33756400-33757200	Genic enhancers	Brain Substantia Nigra	brain
50	chr2:33756400-33757200	Enhancers	Fetal Muscle Leg	muscle

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