Variant report

Variant	rs6790726
Chromosome Location	chr3:150264428-150264429
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	TBP	chr3:150263849-150265094	K562	blood:	n/a	n/a
2	TEAD4	chr3:150263186-150265203	K562	blood:	n/a	n/a
3	MAX	chr3:150263783-150265166	K562	blood:	n/a	chr3:150263942-150263952 chr3:150264268-150264278
4	TAF1	chr3:150263244-150264969	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr3:150264064-150265482	IMR90	lung:	n/a	n/a
6	TCF12	chr3:150264182-150264628	H1-hESC	embryonic stem cell:	n/a	n/a
7	HA-E2F1	chr3:150263753-150264935	MCF-7	breast:	n/a	chr3:150264415-150264424 chr3:150264431-150264438 chr3:150264433-150264448 chr3:150264173-150264188 chr3:150264424-150264441 chr3:150264427-150264438 chr3:150264015-150264024 chr3:150264427-150264438 chr3:150264424-150264441 chr3:150264267-150264276 chr3:150264424-150264441
8	POLR2A	chr3:150263627-150265505	HL-60	blood:	n/a	n/a
9	PAX5	chr3:150264283-150264709	GM12892	blood:	n/a	chr3:150264415-150264424 chr3:150264455-150264464
10	POLR2A	chr3:150264068-150264827	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:150263797-150264818	ECC-1	luminal epithelium:	n/a	n/a
12	THAP1	chr3:150264294-150264454	K562	blood:	n/a	n/a
13	TEAD4	chr3:150263994-150264487	A549	lung:	n/a	n/a
14	YY1	chr3:150263699-150265014	ECC-1	luminal epithelium:	n/a	chr3:150264579-150264599 chr3:150264267-150264276 chr3:150264204-150264213 chr3:150264015-150264024 chr3:150264010-150264024 chr3:150264341-150264352
15	POLR2A	chr3:150263664-150265431	K562	blood:	n/a	n/a
16	YY1	chr3:150263663-150264940	K562	blood:	n/a	chr3:150264579-150264599 chr3:150264267-150264276 chr3:150264204-150264213 chr3:150264015-150264024 chr3:150264010-150264024 chr3:150264341-150264352
17	ATF2	chr3:150263834-150264970	GM12878	blood:	n/a	n/a
18	CREB1	chr3:150264071-150264713	A549	lung:	n/a	n/a
19	POLR2A	chr3:150255826-150265588	K562	blood:	n/a	n/a
20	CREB1	chr3:150264003-150264938	ECC-1	luminal epithelium:	n/a	n/a
21	YY1	chr3:150263760-150264952	K562	blood:	n/a	chr3:150264579-150264599 chr3:150264267-150264276 chr3:150264204-150264213 chr3:150264015-150264024 chr3:150264010-150264024 chr3:150264341-150264352
22	SIN3AK20	chr3:150263855-150265175	MCF-7	breast:	n/a	n/a
23	HCFC1	chr3:150263461-150265366	K562	blood:	n/a	n/a
24	CEBPD	chr3:150264051-150264624	HepG2	liver:	n/a	n/a
25	MAFK	chr3:150264110-150264544	IMR90	lung:	n/a	chr3:150264296-150264313
26	NFIC	chr3:150263824-150264885	ECC-1	luminal epithelium:	n/a	n/a
27	JUND	chr3:150264051-150264867	H1-hESC	embryonic stem cell:	n/a	n/a
28	CREB1	chr3:150264063-150264949	ECC-1	luminal epithelium:	n/a	n/a
29	REST	chr3:150264316-150264834	PFSK-1	brain:	n/a	n/a
30	POLR2A	chr3:150263575-150264779	HepG2	liver:	n/a	n/a
31	PBX3	chr3:150263955-150264983	A549	lung:	n/a	n/a
32	RCOR1	chr3:150264079-150265001	K562	blood:	n/a	n/a
33	ZC3H11A	chr3:150264035-150264852	K562	blood:	n/a	n/a
34	SIN3AK20	chr3:150263410-150265449	MCF-7	breast:	n/a	n/a
35	SPI1	chr3:150264125-150264436	K562	blood:	n/a	chr3:150264226-150264239 chr3:150264230-150264237
36	MBD4	chr3:150264294-150265112	HepG2	liver:	n/a	n/a
37	TCF12	chr3:150263454-150265227	ECC-1	luminal epithelium:	n/a	chr3:150265025-150265032 chr3:150263936-150263946
38	RFX5	chr3:150264103-150264698	HepG2	liver:	n/a	n/a
39	USF1	chr3:150264321-150264709	A549	lung:	n/a	n/a
40	HMGN3	chr3:150263333-150264556	K562	blood:	n/a	n/a
41	BCLAF1	chr3:150263692-150265017	GM12878	blood:	n/a	chr3:150263983-150263996 chr3:150263794-150263807 chr3:150264455-150264464 chr3:150264018-150264031
42	POLR2A	chr3:150263756-150265377	HUVEC	blood vessel:	n/a	n/a
43	FOXP2	chr3:150264044-150264630	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr3:150263768-150265525	K562	blood:	n/a	n/a
45	YY1	chr3:150263533-150265206	SK-N-SH	brain:	n/a	chr3:150264579-150264599 chr3:150264267-150264276 chr3:150264204-150264213 chr3:150264015-150264024 chr3:150264010-150264024 chr3:150264341-150264352
46	MAX	chr3:150263626-150265019	H1-hESC	embryonic stem cell:	n/a	chr3:150263942-150263952 chr3:150264268-150264278
47	JUN	chr3:150263787-150266082	K562	blood:	n/a	chr3:150265419-150265431
48	NFIC	chr3:150264063-150264740	HepG2	liver:	n/a	n/a
49	MAX	chr3:150263824-150265062	HUVEC	blood vessel:	n/a	chr3:150263942-150263952 chr3:150264268-150264278
50	POLR2A	chr3:150264419-150265038	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:75012146..75012773-chr3:150263699..150264695,2	NB4	blood:
2	chr19:15235951..15236569-chr3:150264210..150264994,2	Hela-S3	cervix:
3	chr3:150124887..150127352-chr3:150262732..150264840,2	MCF-7	breast:
4	chr3:150262222..150264859-chr3:150319269..150321349,2	K562	blood:
5	chr15:81293201..81293823-chr3:150263730..150264432,2	Hela-S3	cervix:
6	chr3:150264211..150267828-chr3:150269131..150272633,7	MCF-7	breast:
7	chr10:30722418..30723302-chr3:150263773..150264650,2	Hela-S3	cervix:
8	chr3:73159572..73160366-chr3:150263764..150264740,2	Hela-S3	cervix:
9	chr3:150263328..150264962-chr3:169490309..169491888,2	MCF-7	breast:
10	chr3:150261800..150265866-chr3:150477764..150484308,7	MCF-7	breast:
11	chr3:150260773..150268334-chr3:150317152..150324883,17	K562	blood:
12	chr3:150262524..150267011-chr3:150319982..150323189,4	MCF-7	breast:
13	chr17:15902603..15903275-chr3:150264080..150264900,2	Hela-S3	cervix:
14	chr3:150264199..150264733-chr5:139936637..139937560,2	HCT-116	colon:
15	chr15:65902956..65903827-chr3:150263873..150264800,2	Hela-S3	cervix:
16	chr3:150264346..150265088-chr5:61707993..61708938,2	Hela-S3	cervix:
17	chr13:51484081..51484759-chr3:150264254..150264982,2	Hela-S3	cervix:
18	chr10:69834591..69835099-chr3:150263835..150264657,2	NB4	blood:
19	chr3:150124642..150128245-chr3:150263775..150265951,4	K562	blood:
20	chr3:149955042..149957840-chr3:150262787..150265326,3	MCF-7	breast:
21	chr3:149687147..149691013-chr3:150264416..150266295,3	MCF-7	breast:
22	chr11:11862760..11863701-chr3:150263846..150264451,2	Hela-S3	cervix:
23	chr11:62609028..62609626-chr3:150264298..150264809,2	NB4	blood:
24	chr1:144533737..144534539-chr3:150263791..150264484,3	Hela-S3	cervix:
25	chr3:150122822..150130151-chr3:150261910..150267967,8	K562	blood:
26	chr11:47869268..47869874-chr3:150264298..150265208,2	NB4	blood:
27	chr3:150259884..150269236-chr3:150319275..150325391,10	MCF-7	breast:
28	chr3:150124697..150131961-chr3:150259924..150266159,12	MCF-7	breast:
29	chr3:150263797..150265530-chr3:150478854..150481327,3	MCF-7	breast:
30	chr17:4852602..4853571-chr3:150264064..150264635,2	Hela-S3	cervix:
31	chr3:150262857..150265948-chr3:150299481..150302314,3	K562	blood:

Variant related genes	Relation type
SERP1	TF binding region
EIF2A	TF binding region
ENSG00000144895	Chromatin interaction
ENSG00000214941	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000011295	Chromatin interaction
ENSG00000268175	Chromatin interaction
ENSG00000070087	Chromatin interaction
ENSG00000244265	Chromatin interaction
ENSG00000196428	Chromatin interaction
ENSG00000244541	Chromatin interaction
ENSG00000107968	Chromatin interaction
ENSG00000085274	Chromatin interaction
ENSG00000182180	Chromatin interaction
ENSG00000170242	Chromatin interaction
ENSG00000120742	Chromatin interaction
ENSG00000074621	Chromatin interaction
ENSG00000086200	Chromatin interaction
ENSG00000030066	Chromatin interaction
ENSG00000138614	Chromatin interaction
ENSG00000213523	Chromatin interaction
ENSG00000181788	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000105135	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000108515	Chromatin interaction
ENSG00000227540	Chromatin interaction
ENSG00000148634	Chromatin interaction
ENSG00000233672	Chromatin interaction
ENSG00000140406	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1133494	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13071114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs13097283	0.81[YRI][hapmap]
rs14434	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1464517	0.82[YRI][hapmap]
rs1818788	0.81[ASN][1000 genomes]
rs1915942	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1915943	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2049229	0.91[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2090916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2204113	0.82[JPT][hapmap]
rs2868945	0.86[CEU][hapmap];0.81[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	0.88[EUR][1000 genomes]
rs6440683	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6440685	0.81[YRI][hapmap]
rs6440688	0.81[YRI][hapmap]
rs6764672	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6779448	0.80[AFR][1000 genomes]
rs6787881	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6798173	0.86[YRI][hapmap]
rs7374917	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7628889	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7631671	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7638500	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7642917	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8052	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]
rs9289818	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289821	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs954068	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809820	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9819287	0.81[ASN][1000 genomes]
rs9820529	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9865177	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9871517	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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
rs6790726	EIF2A	cis	Artery Aorta	GTEx
rs6790726	EIF2A	cis	Artery Tibial	GTEx
rs6790726	EIF2A	cis	Esophagus Muscularis	GTEx
rs6790726	EIF2A	cis	lung	GTEx
rs6790726	EIF2A	cis	Thyroid	GTEx
rs6790726	EIF2A	cis	Adipose Subcutaneous	GTEx
rs6790726	EIF2A	cis	Nerve Tibial	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	chr3:150262200-150265000	Active TSS	Brain Angular Gyrus	brain
4	chr3:150262200-150265400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr3:150262200-150265600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:150262200-150265600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:150262200-150265800	Active TSS	GM12878-XiMat	blood
8	chr3:150262400-150265000	Active TSS	Brain Anterior Caudate	brain
9	chr3:150262400-150265000	Active TSS	Stomach Smooth Muscle	stomach
10	chr3:150262400-150265600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr3:150262400-150265600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:150262400-150265600	Active TSS	Fetal Intestine Large	intestine
13	chr3:150262400-150265600	Active TSS	HSMMtube	muscle
14	chr3:150262400-150265600	Active TSS	NHLF	lung
15	chr3:150262600-150265000	Active TSS	Fetal Intestine Small	intestine
16	chr3:150262600-150265000	Active TSS	Fetal Thymus	thymus
17	chr3:150262600-150265200	Active TSS	Fetal Stomach	stomach
18	chr3:150262600-150265400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr3:150262600-150265400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:150262600-150265400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:150262600-150265400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:150262600-150265400	Active TSS	Colonic Mucosa	Colon
23	chr3:150262600-150265400	Active TSS	Fetal Muscle Leg	muscle
24	chr3:150262600-150265400	Active TSS	Left Ventricle	heart
25	chr3:150262600-150265400	Active TSS	Ovary	ovary
26	chr3:150262600-150265400	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr3:150262600-150265400	Active TSS	Stomach Mucosa	stomach
28	chr3:150262600-150265600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr3:150262600-150265600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:150262600-150265600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:150262600-150265600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:150262600-150265600	Active TSS	Right Ventricle	heart
33	chr3:150262600-150265800	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr3:150262600-150265800	Active TSS	HMEC	breast
35	chr3:150262600-150265800	Active TSS	HSMM	muscle
36	chr3:150262600-150266400	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr3:150262800-150265000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:150262800-150265000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:150262800-150265000	Active TSS	Liver	Liver
40	chr3:150262800-150265000	Active TSS	Brain Cingulate Gyrus	brain
41	chr3:150262800-150265000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr3:150262800-150265000	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr3:150262800-150265000	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr3:150262800-150265000	Active TSS	HUVEC	blood vessel
45	chr3:150262800-150265000	Active TSS	NH-A	brain
46	chr3:150262800-150265200	Active TSS	Colon Smooth Muscle	Colon
47	chr3:150262800-150265200	Active TSS	Fetal Kidney	kidney
48	chr3:150262800-150265200	Active TSS	Thymus	Thymus
49	chr3:150262800-150265400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:150262800-150265400	Active TSS	Placenta	Placenta

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