Variant report

Variant	rs954068
Chromosome Location	chr3:150265383-150265384
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	CEBPB	chr3:150264064-150265482	IMR90	lung:	n/a	n/a
2	POLR2A	chr3:150263627-150265505	HL-60	blood:	n/a	n/a
3	POLR2A	chr3:150263664-150265431	K562	blood:	n/a	n/a
4	POLR2A	chr3:150255826-150265588	K562	blood:	n/a	n/a
5	SIN3AK20	chr3:150263410-150265449	MCF-7	breast:	n/a	n/a
6	POLR2A	chr3:150263768-150265525	K562	blood:	n/a	n/a
7	JUN	chr3:150263787-150266082	K562	blood:	n/a	chr3:150265419-150265431
8	STAT3	chr3:150265346-150265479	MCF10A-Er-Src	breast:	n/a	chr3:150265464-150265476
9	POLR2A	chr3:150262889-150265615	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:150263964-150265398	K562	blood:	n/a	n/a
11	MXI1	chr3:150263075-150265407	IMR90	lung:	n/a	chr3:150263936-150263945
12	POLR2A	chr3:150263265-150265384	PBDE	blood:	n/a	n/a
13	ELK4	chr3:150264228-150265428	Hela-S3	cervix:	n/a	chr3:150264455-150264463 chr3:150264455-150264464 chr3:150264454-150264465
14	ATF1	chr3:150264166-150265491	K562	blood:	n/a	n/a
15	STAT3	chr3:150265279-150265753	MCF10A-Er-Src	breast:	n/a	chr3:150265464-150265476
16	FOS	chr3:150265346-150265538	MCF10A-Er-Src	breast:	n/a	chr3:150265419-150265431
17	REST	chr3:150263103-150265500	H1-neurons	neurons:	n/a	chr3:150264061-150264074
18	MYC	chr3:150264202-150265716	MCF10A-Er-Src	breast:	n/a	chr3:150264268-150264278
19	MYC	chr3:150263847-150265547	MCF10A-Er-Src	breast:	n/a	chr3:150263942-150263952 chr3:150264268-150264278
20	NFE2	chr3:150265316-150265513	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:150263870-150265509	HUVEC	blood vessel:	n/a	n/a
22	HEY1	chr3:150263709-150265406	K562	blood:	n/a	chr3:150264136-150264151 chr3:150264103-150264118 chr3:150264017-150264032 chr3:150264340-150264355 chr3:150264182-150264197
23	GTF2F1	chr3:150264123-150265474	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr3:150263012-150265871	MCF10A-Er-Src	breast:	n/a	n/a
25	MYC	chr3:150263477-150265502	K562	blood:	n/a	chr3:150263942-150263952 chr3:150264268-150264278
26	POLR2A	chr3:150263935-150265636	SK-N-SH	brain:	n/a	n/a
27	FOS	chr3:150265276-150265526	MCF10A-Er-Src	breast:	n/a	chr3:150265419-150265431
28	EP300	chr3:150264171-150265391	K562	blood:	n/a	chr3:150264205-150264221 chr3:150264205-150264214 chr3:150264456-150264463
29	TBL1XR1	chr3:150264058-150265484	K562	blood:	n/a	n/a
30	E2F4	chr3:150265338-150265746	MCF10A-Er-Src	breast:	n/a	chr3:150265477-150265485 chr3:150265477-150265485
31	CEBPB	chr3:150265127-150265525	K562	blood:	n/a	n/a
32	EP300	chr3:150264120-150265401	GM12878	blood:	n/a	chr3:150264205-150264221 chr3:150264205-150264214 chr3:150264456-150264463
33	MXI1	chr3:150261672-150265743	SK-N-SH	brain:	n/a	chr3:150263936-150263945
34	POLR2A	chr3:150263173-150265470	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:150263870-150265926	MCF10A-Er-Src	breast:	n/a	n/a
36	CEBPB	chr3:150264191-150265632	A549	lung:	n/a	n/a
37	RFX5	chr3:150263161-150265534	Hela-S3	cervix:	n/a	n/a
38	CREB1	chr3:150263160-150265405	GM12878	blood:	n/a	n/a
39	GABPA	chr3:150263763-150265576	MCF-7	breast:	n/a	chr3:150264411-150264425 chr3:150264414-150264425 chr3:150264416-150264425
40	CEBPB	chr3:150264087-150265563	K562	blood:	n/a	n/a
41	RCOR1	chr3:150263232-150265435	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr3:150265285-150265435	HepG2	liver:	n/a	n/a
43	MAZ	chr3:150263142-150265419	IMR90	lung:	n/a	chr3:150263942-150263952 chr3:150264268-150264278
44	POLR2A	chr3:150263221-150265609	GM12891	blood:	n/a	n/a
45	SMARCC1	chr3:150263265-150265617	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr3:150263206-150266133	IMR90	lung:	n/a	n/a
47	MYC	chr3:150263450-150265394	K562	blood:	n/a	chr3:150263942-150263952 chr3:150264268-150264278
48	POLR2A	chr3:150263370-150265405	Raji	blood:	n/a	n/a
49	CHD1	chr3:150260657-150265744	IMR90	lung:	n/a	chr3:150264431-150264438
50	MYC	chr3:150263964-150265448	K562	blood:	n/a	chr3:150264268-150264278

No.	Distal block	Cell Line	Cell type
1	chr3:150264211..150267828-chr3:150269131..150272633,7	MCF-7	breast:
2	chr3:150264606..150266340-chr3:150304778..150306324,2	MCF-7	breast:
3	chr3:150261800..150265866-chr3:150477764..150484308,7	MCF-7	breast:
4	chr3:150260773..150268334-chr3:150317152..150324883,17	K562	blood:
5	chr3:150262524..150267011-chr3:150319982..150323189,4	MCF-7	breast:
6	chr3:150264699..150266446-chr3:150353006..150354618,2	K562	blood:
7	chr3:150124642..150128245-chr3:150263775..150265951,4	K562	blood:
8	chr3:149687147..149691013-chr3:150264416..150266295,3	MCF-7	breast:
9	chr3:150265254..150267392-chr3:150344377..150346333,2	K562	blood:
10	chr3:150122822..150130151-chr3:150261910..150267967,8	K562	blood:
11	chr3:150089195..150090821-chr3:150265042..150267654,2	MCF-7	breast:
12	chr3:150259884..150269236-chr3:150319275..150325391,10	MCF-7	breast:
13	chr3:150124697..150131961-chr3:150259924..150266159,12	MCF-7	breast:
14	chr3:150263797..150265530-chr3:150478854..150481327,3	MCF-7	breast:
15	chr3:150262857..150265948-chr3:150299481..150302314,3	K562	blood:

Variant related genes	Relation type
EIF2A	TF binding region
SERP1	TF binding region
ENSG00000244265	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000268175	Chromatin interaction
ENSG00000070087	Chromatin interaction
ENSG00000144895	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000181788	Chromatin interaction
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1133494	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs14434	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1818788	0.81[ASN][1000 genomes]
rs1915942	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1915943	0.81[ASN][1000 genomes]
rs2049229	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2090916	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2868945	0.82[EUR][1000 genomes]
rs2868946	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2868947	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4681631	0.87[EUR][1000 genomes]
rs6440683	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6764672	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6779448	0.80[AFR][1000 genomes]
rs6787881	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6790726	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374917	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7628889	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7631671	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7638500	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7642917	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8052	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289818	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289821	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9819287	0.81[ASN][1000 genomes]
rs9820529	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9865177	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9871517	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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
rs954068	EIF2A	cis	Adipose Subcutaneous	GTEx
rs954068	EIF2A	cis	Artery Aorta	GTEx
rs954068	EIF2A	cis	Artery Tibial	GTEx
rs954068	EIF2A	cis	Esophagus Muscularis	GTEx
rs954068	EIF2A	cis	Nerve Tibial	GTEx
rs954068	EIF2A	cis	lung	GTEx
rs954068	EIF2A	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150262000-150266000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:150262000-150266200	Active TSS	Psoas Muscle	Psoas
3	chr3:150262200-150265400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:150262200-150265600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:150262200-150265600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:150262200-150265800	Active TSS	GM12878-XiMat	blood
7	chr3:150262400-150265600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr3:150262400-150265600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:150262400-150265600	Active TSS	Fetal Intestine Large	intestine
10	chr3:150262400-150265600	Active TSS	HSMMtube	muscle
11	chr3:150262400-150265600	Active TSS	NHLF	lung
12	chr3:150262600-150265400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr3:150262600-150265400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:150262600-150265400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:150262600-150265400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:150262600-150265400	Active TSS	Colonic Mucosa	Colon
17	chr3:150262600-150265400	Active TSS	Fetal Muscle Leg	muscle
18	chr3:150262600-150265400	Active TSS	Left Ventricle	heart
19	chr3:150262600-150265400	Active TSS	Ovary	ovary
20	chr3:150262600-150265400	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr3:150262600-150265400	Active TSS	Stomach Mucosa	stomach
22	chr3:150262600-150265600	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr3:150262600-150265600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:150262600-150265600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:150262600-150265600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:150262600-150265600	Active TSS	Right Ventricle	heart
27	chr3:150262600-150265800	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:150262600-150265800	Active TSS	HMEC	breast
29	chr3:150262600-150265800	Active TSS	HSMM	muscle
30	chr3:150262600-150266400	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr3:150262800-150265400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:150262800-150265400	Active TSS	Placenta	Placenta
33	chr3:150262800-150265400	Active TSS	Hela-S3	cervix
34	chr3:150262800-150265600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:150262800-150265600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:150262800-150265600	Active TSS	Aorta	Aorta
37	chr3:150262800-150265600	Active TSS	A549	lung
38	chr3:150262800-150266200	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr3:150262800-150266400	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr3:150262800-150266400	Active TSS	NHDF-Ad	bronchial
41	chr3:150263000-150265400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr3:150263000-150265400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:150263000-150265400	Active TSS	Muscle Satellite Cultured Cells	--
44	chr3:150263000-150265400	Active TSS	NHEK	skin
45	chr3:150263000-150265800	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr3:150263000-150265800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr3:150263000-150266000	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr3:150263000-150266200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:150263200-150265400	Active TSS	Fetal Muscle Trunk	muscle
50	chr3:150263200-150265600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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