Variant report

Variant	rs8052
Chromosome Location	chr3:150259942-150259943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:150255826-150265588	K562	blood:	n/a	n/a
2	POLR2A	chr3:150259321-150260047	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA3	chr3:150259920-150260076	SH-SY5Y	brain:	n/a	n/a
4	POLR2A	chr3:150259506-150261877	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:150258860-150261404	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr3:150259612-150260083	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:150258656-150262136	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:150255233-150259949	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr3:150258901-150261922	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:150259942-150259952	K562	blood:	n/a	n/a
11	POLR2A	chr3:150255232-150262283	IMR90	lung:	n/a	n/a
12	POLR2A	chr3:150259633-150261315	Hela-S3	cervix:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150239109..150240851-chr3:150258863..150260521,2	K562	blood:
2	chr3:150258291..150260561-chr3:150340195..150342969,2	K562	blood:
3	chr3:150249048..150250723-chr3:150259118..150261597,2	MCF-7	breast:
4	chr3:149957085..149958693-chr3:150257954..150260246,2	K562	blood:
5	chr3:150257534..150260466-chr3:150320430..150322840,2	MCF-7	breast:
6	chr3:150245282..150248220-chr3:150257440..150261606,3	K562	blood:
7	chr3:150123749..150128774-chr3:150257653..150260778,4	K562	blood:
8	chr3:150259884..150269236-chr3:150319275..150325391,10	MCF-7	breast:
9	chr3:150259795..150261477-chr3:150319627..150322330,2	K562	blood:
10	chr3:150259312..150261315-chr3:150274243..150276592,2	MCF-7	breast:
11	chr3:150124697..150131961-chr3:150259924..150266159,12	MCF-7	breast:
12	chr3:150124970..150128067-chr3:150255521..150260778,6	K562	blood:

No data

Variant related genes	Relation type
EIF2A	TF binding region
ENSG00000120742	Chromatin interaction
ENSG00000196428	Chromatin interaction
ENSG00000198843	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1133494	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12695957	0.87[AFR][1000 genomes]
rs13071114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs14434	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs16862785	0.84[YRI][hapmap]
rs1915942	0.83[EUR][1000 genomes]
rs1915943	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2049229	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2090916	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2204113	0.82[JPT][hapmap]
rs2868945	0.87[CEU][hapmap]
rs2868946	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2868947	0.91[ASN][1000 genomes]
rs4681631	0.91[EUR][1000 genomes]
rs6440683	0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6440685	0.93[ASW][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6440688	0.81[LWK][hapmap];0.96[YRI][hapmap]
rs6764672	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6787881	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6790726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7374917	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7628889	0.95[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7631671	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7638500	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7642917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9289818	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289821	0.83[EUR][1000 genomes]
rs954068	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9809820	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9820529	0.90[AMR][1000 genomes]
rs9865177	0.83[EUR][1000 genomes]
rs9871517	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8052	EIF2A	cis	Thyroid	GTEx
rs8052	COMMD2	cis	cerebellum	SCAN
rs8052	EIF2A	cis	lung	GTEx
rs8052	EIF2A	cis	multi-tissue	Pritchard
rs8052	EIF2A	cis	Artery Tibial	GTEx
rs8052	TM4SF4	cis	parietal	SCAN
rs8052	EIF2A	cis	Esophagus Muscularis	GTEx
rs8052	EIF2A	cis	normal skin	skin_eQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150246200-150260600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:150246400-150261800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:150246400-150262600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:150248400-150263200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:150248800-150262000	Weak transcription	Thymus	Thymus
6	chr3:150249600-150260400	Weak transcription	GM12878-XiMat	blood
7	chr3:150254400-150262000	Weak transcription	Fetal Intestine Small	intestine
8	chr3:150254400-150262600	Weak transcription	Fetal Stomach	stomach
9	chr3:150254800-150261400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:150255000-150261000	Weak transcription	Fetal Brain Male	brain
11	chr3:150255200-150260600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:150255200-150262600	Weak transcription	Right Ventricle	heart
13	chr3:150255400-150261800	Weak transcription	Brain Substantia Nigra	brain
14	chr3:150256000-150263200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:150256000-150263200	Weak transcription	Lung	lung
16	chr3:150256200-150260800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:150256400-150260600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:150256600-150260200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:150256600-150260600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:150256600-150260600	Weak transcription	Brain Anterior Caudate	brain
21	chr3:150256600-150262800	Weak transcription	Aorta	Aorta
22	chr3:150256800-150260200	Weak transcription	Osteobl	bone
23	chr3:150256800-150260600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:150256800-150260600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:150256800-150261200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:150256800-150262600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:150256800-150263200	Weak transcription	Esophagus	oesophagus
28	chr3:150256800-150263200	Weak transcription	Gastric	stomach
29	chr3:150257000-150262600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:150257000-150262600	Weak transcription	Ovary	ovary
31	chr3:150257200-150260600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:150257200-150262600	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:150257600-150261600	Weak transcription	Stomach Mucosa	stomach
34	chr3:150257600-150262000	Weak transcription	Fetal Kidney	kidney
35	chr3:150257600-150263200	Weak transcription	Pancreas	Pancrea
36	chr3:150258000-150260600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:150258000-150261200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:150258000-150261200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:150258200-150260800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr3:150258200-150260800	Weak transcription	Fetal Intestine Large	intestine
41	chr3:150258200-150261400	Weak transcription	NHLF	lung
42	chr3:150258400-150260400	Weak transcription	HepG2	liver
43	chr3:150258400-150260600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:150258400-150261200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:150258400-150262400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:150258400-150262400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr3:150258600-150260000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr3:150258600-150261200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:150258600-150262400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:150258800-150260800	Strong transcription	Liver	Liver

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