Variant report

Variant	rs9289821
Chromosome Location	chr3:150318067-150318068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:150317428-150318345	H1-hESC	embryonic stem cell:	n/a	n/a
2	EP300	chr3:150317458-150318147	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:150317444-150318117	K562	blood:	n/a	n/a
4	JUND	chr3:150317410-150318192	HCT-116	colon:	n/a	n/a
5	GATA3	chr3:150317490-150318115	MCF-7	breast:	n/a	n/a
6	TCF12	chr3:150317409-150318084	SK-N-SH	brain:	n/a	n/a
7	FOSL1	chr3:150317422-150318154	HCT-116	colon:	n/a	n/a
8	ARID3A	chr3:150317510-150318801	K562	blood:	n/a	n/a
9	FOSL1	chr3:150317400-150318251	HCT-116	colon:	n/a	n/a
10	JUND	chr3:150317499-150318069	H1-hESC	embryonic stem cell:	n/a	n/a
11	TEAD4	chr3:150317646-150318076	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr3:150317429-150318079	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr3:150316259-150319258	GM12878	blood:	n/a	n/a
14	MTA3	chr3:150316205-150318380	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:150317333-150318396	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:150317423-150318428	GM12878	blood:	n/a	n/a
17	CEBPB	chr3:150317395-150318698	HCT-116	colon:	n/a	chr3:150318523-150318534
18	SP1	chr3:150317408-150318176	HCT-116	colon:	n/a	n/a
19	TEAD4	chr3:150317604-150318149	SK-N-SH	brain:	n/a	n/a
20	GATA3	chr3:150317423-150318158	SK-N-SH	brain:	n/a	n/a
21	CHD1	chr3:150317836-150318765	GM12878	blood:	n/a	n/a
22	NFIC	chr3:150317415-150318150	SK-N-SH	brain:	n/a	n/a
23	JUND	chr3:150317443-150318140	HCT-116	colon:	n/a	n/a
24	SP1	chr3:150317409-150318237	HCT-116	colon:	n/a	n/a
25	YY1	chr3:150317699-150318088	H1-hESC	embryonic stem cell:	n/a	n/a
26	CBX3	chr3:150317414-150318068	HCT-116	colon:	n/a	n/a
27	RCOR1	chr3:150317336-150318403	IMR90	lung:	n/a	n/a
28	TEAD4	chr3:150317491-150318091	ECC-1	luminal epithelium:	n/a	n/a
29	GATA3	chr3:150317546-150318104	MCF-7	breast:	n/a	n/a
30	TCF12	chr3:150317423-150318141	SK-N-SH	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150260773..150268334-chr3:150317152..150324883,17	K562	blood:
2	chr3:150262918..150266548-chr3:150316977..150319040,3	K562	blood:
3	chr3:150317577..150319249-chr3:150479871..150481805,2	MCF-7	breast:
4	chr3:150316261..150319464-chr3:150319733..150322939,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198843	TF binding region
ENSG00000198843	Chromatin interaction
ENSG00000181788	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000144895	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1133494	0.89[ASN][1000 genomes]
rs14434	0.89[ASN][1000 genomes]
rs1818788	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915942	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915943	1.00[ASN][1000 genomes]
rs2049229	0.89[ASN][1000 genomes]
rs2090916	0.89[ASN][1000 genomes]
rs2204112	0.88[ASN][1000 genomes]
rs2868945	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2868946	0.89[ASN][1000 genomes]
rs2868947	0.89[ASN][1000 genomes]
rs6440683	0.89[ASN][1000 genomes]
rs6764672	0.83[EUR][1000 genomes]
rs6787881	0.82[EUR][1000 genomes]
rs6790726	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7374917	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7628889	0.89[ASN][1000 genomes]
rs7631671	0.89[ASN][1000 genomes]
rs7638500	0.89[ASN][1000 genomes]
rs7642917	0.89[ASN][1000 genomes]
rs8052	0.83[EUR][1000 genomes]
rs9289818	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs954068	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9809820	0.98[ASN][1000 genomes]
rs9819287	1.00[ASN][1000 genomes]
rs9836797	0.96[ASN][1000 genomes]
rs9858682	0.81[EUR][1000 genomes]
rs9865177	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871517	0.87[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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9289821	EIF2A	cis	Artery Aorta	GTEx
rs9289821	EIF2A	cis	lung	GTEx
rs9289821	EIF2A	cis	Thyroid	GTEx
rs9289821	EIF2A	cis	Artery Tibial	GTEx
rs9289821	EIF2A	cis	Esophagus Muscularis	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150265600-150320600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:150265600-150320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:150295600-150318600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:150301600-150320200	Weak transcription	Small Intestine	intestine
5	chr3:150302400-150320000	Weak transcription	Brain Germinal Matrix	brain
6	chr3:150303600-150319200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:150303800-150318800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:150303800-150318800	Weak transcription	Fetal Lung	lung
9	chr3:150303800-150320000	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:150303800-150320000	Weak transcription	Fetal Brain Female	brain
11	chr3:150303800-150320000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:150303800-150320800	Weak transcription	Lung	lung
13	chr3:150303800-150320800	Weak transcription	Spleen	Spleen
14	chr3:150304000-150320000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:150304000-150320000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:150304000-150320000	Weak transcription	Fetal Stomach	stomach
17	chr3:150304000-150320600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:150304400-150320000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:150304400-150320200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:150304400-150320600	Weak transcription	Ovary	ovary
21	chr3:150304600-150318600	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:150304800-150320400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:150305000-150318400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:150306200-150320000	Weak transcription	Left Ventricle	heart
25	chr3:150306400-150318200	Weak transcription	Primary T cells from cord blood	blood
26	chr3:150306400-150319000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:150312800-150320000	Weak transcription	Fetal Intestine Small	intestine
28	chr3:150315600-150319000	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:150315600-150319200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:150315600-150320000	Enhancers	HMEC	breast
31	chr3:150316200-150318400	Enhancers	HSMM	muscle
32	chr3:150316200-150318600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:150316200-150318800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:150316200-150318800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:150316200-150319000	Enhancers	Placenta	Placenta
36	chr3:150316400-150318800	Enhancers	HUVEC	blood vessel
37	chr3:150316400-150319000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr3:150316400-150319800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:150316600-150318200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:150316600-150318800	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr3:150316600-150318800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:150316800-150318200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:150316800-150318800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:150316800-150318800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:150316800-150318800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:150316800-150318800	Flanking Active TSS	GM12878-XiMat	blood
47	chr3:150316800-150319200	Enhancers	H1 Cell Line	embryonic stem cell
48	chr3:150316800-150319200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:150316800-150319200	Enhancers	Placenta Amnion	Placenta Amnion
50	chr3:150316800-150319400	Enhancers	HUES64 Cell Line	embryonic stem cell

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