Variant report

Variant	rs17027798
Chromosome Location	chr4:152597540-152597541
allele	A/G
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	FOS	chr4:152597506-152597809	MCF10A-Er-Src	breast:	n/a	chr4:152597636-152597647
2	NFIC	chr4:152597390-152597996	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr4:152597527-152597546	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr4:152597496-152597750	SK-N-SH_RA	brain:	n/a	n/a
5	SIN3AK20	chr4:152597459-152597813	SK-N-SH	brain:	n/a	n/a
6	FOSL2	chr4:152597326-152598003	SK-N-SH	brain:	n/a	n/a
7	TCF12	chr4:152597271-152598043	SK-N-SH	brain:	n/a	chr4:152598012-152598019
8	PBX3	chr4:152597444-152597946	SK-N-SH	brain:	n/a	n/a
9	STAT3	chr4:152597469-152597822	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr4:152597521-152597811	MCF10A-Er-Src	breast:	n/a	chr4:152597636-152597647
11	FOS	chr4:152597429-152597876	HUVEC	blood vessel:	n/a	chr4:152597636-152597647
12	PBX3	chr4:152597346-152598003	SK-N-SH	brain:	n/a	n/a
13	TCF12	chr4:152597264-152598091	SK-N-SH	brain:	n/a	chr4:152598012-152598019
14	FOS	chr4:152597496-152597827	MCF10A-Er-Src	breast:	n/a	chr4:152597636-152597647
15	MAX	chr4:152597386-152597863	SK-N-SH	brain:	n/a	n/a
16	JUND	chr4:152597251-152598313	SK-N-SH	brain:	n/a	chr4:152598205-152598215 chr4:152598205-152598215 chr4:152598205-152598215
17	GATA3	chr4:152597276-152597998	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr4:152597498-152597683	H1-hESC	embryonic stem cell:	n/a	n/a
19	EP300	chr4:152597419-152597794	SK-N-SH_RA	brain:	n/a	n/a
20	FOS	chr4:152597519-152597827	MCF10A-Er-Src	breast:	n/a	chr4:152597636-152597647
21	JUND	chr4:152597393-152597978	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr4:152597410-152597875	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152586811..152588784-chr4:152594944..152597793,2	MCF-7	breast:
2	chr4:152591570..152594728-chr4:152597153..152600543,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM160A1-2	chr4:152595635-152597712	ENSG00000251455.1

Variant related genes	Relation type
PET112	TF binding region
ENSG00000251603	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10007015	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10007167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10019048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10023298	0.86[EUR][1000 genomes]
rs10028410	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10028961	0.86[EUR][1000 genomes]
rs10049728	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10049991	0.86[EUR][1000 genomes]
rs10776524	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1105534	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1105535	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1105536	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11734799	0.81[EUR][1000 genomes]
rs12331037	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs12502055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137669	0.82[EUR][1000 genomes]
rs13138986	0.81[EUR][1000 genomes]
rs13146981	0.81[EUR][1000 genomes]
rs13149588	0.92[CEU][hapmap]
rs1355413	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs1366909	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1511170	0.84[EUR][1000 genomes]
rs17360475	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs1864300	0.85[EUR][1000 genomes]
rs1877187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1896883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2007218	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs2007445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2303866	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2840130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28637056	0.87[EUR][1000 genomes]
rs28710456	0.86[EUR][1000 genomes]
rs3749561	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3749563	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792691	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes]
rs3919716	0.84[EUR][1000 genomes]
rs4383600	0.84[EUR][1000 genomes]
rs4571	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4696104	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696109	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs4696111	0.86[EUR][1000 genomes]
rs4696277	0.93[EUR][1000 genomes]
rs4696283	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4696284	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696285	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696291	0.90[EUR][1000 genomes]
rs4696293	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4696294	0.81[EUR][1000 genomes]
rs55668815	0.86[EUR][1000 genomes]
rs6535809	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6535811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6535812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6535813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535814	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6535815	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6535817	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6535818	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs6535819	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs6535821	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6810860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6817058	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6817586	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs6818667	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823002	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6823194	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823421	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6823462	0.83[EUR][1000 genomes]
rs6825241	0.80[EUR][1000 genomes]
rs6832562	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6833368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6834095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6838966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6840678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6841204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6841783	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6845944	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6846114	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6849050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7439465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749982	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751012	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751014	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7663045	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7667197	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7669977	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs7671651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684350	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7695162	0.92[EUR][1000 genomes]
rs907237	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9307887	0.83[EUR][1000 genomes]
rs9995704	0.85[EUR][1000 genomes]
rs9998462	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755535	chr4:152549395-152609395	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv4551	chr4:152582617-152627367	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1026511	chr4:152593382-152611915	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17027798	PET112L	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152563800-152625200	Weak transcription	Hela-S3	cervix
2	chr4:152567400-152608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:152567800-152609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:152581200-152602800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:152581200-152608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:152585600-152628600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:152585800-152600400	Weak transcription	Gastric	stomach
8	chr4:152585800-152640400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:152586400-152609000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:152589200-152608800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr4:152589200-152619200	Weak transcription	Dnd41	blood
12	chr4:152590400-152601600	Weak transcription	Primary B cells from cord blood	blood
13	chr4:152590600-152597600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:152590600-152609000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr4:152591200-152608600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr4:152591200-152646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:152592000-152598200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:152592200-152608000	Weak transcription	Thymus	Thymus
19	chr4:152592400-152597800	Enhancers	Left Ventricle	heart
20	chr4:152592600-152636400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:152593600-152608000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:152593600-152608800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:152594000-152600400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:152594200-152600400	Weak transcription	Fetal Thymus	thymus
25	chr4:152595200-152598000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:152595200-152598800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:152595200-152611600	Weak transcription	K562	blood
28	chr4:152595600-152602400	Weak transcription	HepG2	liver
29	chr4:152595600-152608600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:152596000-152598000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:152596000-152598200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:152596000-152598200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:152596000-152598200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr4:152596000-152598200	Enhancers	HSMMtube	muscle
35	chr4:152596000-152598200	Enhancers	NH-A	brain
36	chr4:152596000-152599200	Weak transcription	Fetal Kidney	kidney
37	chr4:152596200-152598200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:152596200-152598200	Enhancers	Fetal Muscle Leg	muscle
39	chr4:152596200-152598200	Enhancers	NHDF-Ad	bronchial
40	chr4:152596200-152599600	Weak transcription	Spleen	Spleen
41	chr4:152596200-152608600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:152596200-152624000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr4:152596400-152598000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:152596400-152598000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr4:152596400-152598000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr4:152596400-152598200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:152596400-152598200	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr4:152596400-152598200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:152596400-152598200	Enhancers	Fetal Muscle Trunk	muscle
50	chr4:152596400-152598200	Enhancers	HSMM	muscle

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