Variant report

Variant	rs2868946
Chromosome Location	chr3:150306490-150306491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150306459..150312213-chr3:150319876..150323400,9	MCF-7	breast:
2	chr3:150304290..150306605-chr3:150321050..150322938,2	K562	blood:
3	chr3:150296057..150298158-chr3:150306282..150308103,2	K562	blood:
4	chr3:150295926..150298011-chr3:150304810..150307775,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120742	Chromatin interaction
ENSG00000198843	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1133494	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs14434	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1818788	0.89[ASN][1000 genomes]
rs1915942	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1915943	0.89[ASN][1000 genomes]
rs2049229	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2090916	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2868947	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6440683	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440684	0.84[ASN][1000 genomes]
rs6440685	0.89[EUR][1000 genomes]
rs6764672	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6779448	0.85[AFR][1000 genomes]
rs6787881	0.88[AFR][1000 genomes]
rs6790726	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7374917	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7628889	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631671	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638500	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7642917	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8052	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9289818	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9289820	0.84[ASN][1000 genomes]
rs9289821	0.89[ASN][1000 genomes]
rs954068	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9809820	0.87[ASN][1000 genomes]
rs9819287	0.89[ASN][1000 genomes]
rs9820529	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9836797	0.85[ASN][1000 genomes]
rs9865177	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9871517	0.83[AFR][1000 genomes];0.88[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2868946	EIF2A	cis	Thyroid	GTEx
rs2868946	EIF2A	cis	Esophagus Muscularis	GTEx
rs2868946	EIF2A	cis	Artery Tibial	GTEx
rs2868946	EIF2A	cis	Artery Aorta	GTEx
rs2868946	EIF2A	cis	lung	GTEx
rs2868946	EIF2A	cis	Nerve Tibial	GTEx
rs2868946	EIF2A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

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	chr3:150266000-150307600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:150278000-150306800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:150280200-150307800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:150294200-150314600	Weak transcription	Psoas Muscle	Psoas
7	chr3:150294400-150306600	Weak transcription	Brain Angular Gyrus	brain
8	chr3:150295400-150307200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:150295600-150318600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:150300800-150316200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:150301600-150306600	Strong transcription	GM12878-XiMat	blood
12	chr3:150301600-150320200	Weak transcription	Small Intestine	intestine
13	chr3:150302400-150320000	Weak transcription	Brain Germinal Matrix	brain
14	chr3:150302600-150307600	Weak transcription	NHDF-Ad	bronchial
15	chr3:150303000-150316400	Weak transcription	HUVEC	blood vessel
16	chr3:150303200-150307000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:150303400-150316800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:150303600-150307400	Weak transcription	Stomach Mucosa	stomach
19	chr3:150303600-150308000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr3:150303600-150308000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:150303600-150310400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:150303600-150315600	Weak transcription	HMEC	breast
23	chr3:150303600-150317400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:150303600-150319200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:150303800-150307000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:150303800-150307600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:150303800-150307800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:150303800-150307800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:150303800-150307800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:150303800-150308000	Weak transcription	Aorta	Aorta
31	chr3:150303800-150308600	Weak transcription	Adipose Nuclei	Adipose
32	chr3:150303800-150308800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:150303800-150309400	Weak transcription	Esophagus	oesophagus
34	chr3:150303800-150310000	Weak transcription	Osteobl	bone
35	chr3:150303800-150310600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:150303800-150313800	Weak transcription	Pancreas	Pancrea
37	chr3:150303800-150315600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:150303800-150316200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:150303800-150316400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:150303800-150316400	Weak transcription	NH-A	brain
41	chr3:150303800-150316800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:150303800-150316800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:150303800-150316800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:150303800-150317200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:150303800-150317400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:150303800-150318000	Weak transcription	NHLF	lung
47	chr3:150303800-150318800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:150303800-150318800	Weak transcription	Fetal Lung	lung
49	chr3:150303800-150320000	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:150303800-150320000	Weak transcription	Fetal Brain Female	brain

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