Variant report

Variant	rs202075
Chromosome Location	chr6:13269477-13269478
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	MAX	chr6:13269448-13269621	K562	blood:	n/a	n/a
2	CEBPB	chr6:13269429-13269776	H1-hESC	embryonic stem cell:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
3	JUND	chr6:13269467-13269751	K562	blood:	n/a	n/a
4	TEAD4	chr6:13269306-13269746	K562	blood:	n/a	n/a
5	GTF2F1	chr6:13269448-13269547	H1-hESC	embryonic stem cell:	n/a	chr6:13269486-13269497
6	CEBPB	chr6:13269372-13269855	MCF-7	breast:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
7	FOS	chr6:13269444-13269773	MCF10A-Er-Src	breast:	n/a	n/a
8	TEAD4	chr6:13269316-13269787	HepG2	liver:	n/a	n/a
9	TEAD4	chr6:13269311-13269773	ECC-1	luminal epithelium:	n/a	n/a
10	FOXA1	chr6:13269380-13269701	T-47D	breast:	n/a	n/a
11	NR2F2	chr6:13269266-13269824	MCF-7	breast:	n/a	n/a
12	CEBPB	chr6:13269421-13269768	HepG2	liver:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
13	EP300	chr6:13269419-13269738	Hela-S3	cervix:	n/a	chr6:13269602-13269616
14	ESR1	chr6:13269366-13269647	T-47D	breast:	n/a	n/a
15	CEBPB	chr6:13269409-13269796	K562	blood:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
16	TEAD4	chr6:13269385-13269770	K562	blood:	n/a	n/a
17	CEBPB	chr6:13269253-13269938	MCF-7	breast:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
18	NR2F2	chr6:13269276-13269793	MCF-7	breast:	n/a	n/a
19	STAT3	chr6:13269470-13269670	MCF10A-Er-Src	breast:	n/a	n/a
20	E2F4	chr6:13269430-13269630	MCF10A-Er-Src	breast:	n/a	n/a
21	MYC	chr6:13269458-13269715	MCF10A-Er-Src	breast:	n/a	n/a
22	TEAD4	chr6:13269390-13269786	ECC-1	luminal epithelium:	n/a	n/a
23	GATA3	chr6:13269416-13269868	MCF-7	breast:	n/a	n/a
24	FOS	chr6:13269438-13269767	MCF10A-Er-Src	breast:	n/a	n/a
25	CEBPB	chr6:13269386-13269809	ECC-1	luminal epithelium:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
26	CEBPB	chr6:13269392-13269807	A549	lung:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
27	TEAD4	chr6:13269409-13269807	MCF-7	breast:	n/a	n/a
28	STAT3	chr6:13269445-13269641	MCF10A-Er-Src	breast:	n/a	n/a
29	RFX5	chr6:13269424-13269725	Hela-S3	cervix:	n/a	n/a
30	FOS	chr6:13269409-13269756	MCF10A-Er-Src	breast:	n/a	n/a
31	CEBPD	chr6:13269387-13269858	K562	blood:	n/a	chr6:13269602-13269613
32	TEAD4	chr6:13269439-13269775	H1-hESC	embryonic stem cell:	n/a	n/a
33	FOS	chr6:13269408-13269767	MCF10A-Er-Src	breast:	n/a	n/a
34	ATF3	chr6:13269424-13269766	K562	blood:	n/a	n/a
35	GATA3	chr6:13269286-13269736	T-47D	breast:	n/a	n/a
36	BHLHE40	chr6:13269396-13269596	K562	blood:	n/a	n/a
37	CEBPB	chr6:13269370-13269774	K562	blood:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
38	CEBPB	chr6:13269429-13269784	IMR90	lung:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
39	CEBPB	chr6:13269414-13269790	HepG2	liver:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
40	GATA3	chr6:13269192-13269879	MCF-7	breast:	n/a	n/a
41	GATA3	chr6:13269232-13269765	T-47D	breast:	n/a	n/a
42	CEBPB	chr6:13269398-13269815	Hela-S3	cervix:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
43	CEBPB	chr6:13269429-13269748	A549	lung:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
44	FOXA1	chr6:13269290-13269688	T-47D	breast:	n/a	n/a
45	JUND	chr6:13269346-13269854	T-47D	breast:	n/a	n/a
46	CEBPB	chr6:13269390-13269784	HepG2	liver:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
47	MYC	chr6:13269445-13269718	MCF10A-Er-Src	breast:	n/a	n/a
48	CEBPB	chr6:13269393-13269792	ECC-1	luminal epithelium:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711
49	JUND	chr6:13269450-13269761	H1-hESC	embryonic stem cell:	n/a	n/a
50	CEBPB	chr6:13269406-13269716	K562	blood:	n/a	chr6:13269601-13269612 chr6:13269696-13269713 chr6:13269603-13269614 chr6:13269699-13269711

No.	Distal block	Cell Line	Cell type
1	chr6:13268970..13278598-chr6:13326296..13332818,15	K562	blood:
2	chr6:13266277..13270174-chr6:13278637..13282022,4	MCF-7	breast:
3	chr6:13258559..13263124-chr6:13265994..13271116,8	K562	blood:
4	chr6:13259737..13263124-chr6:13265994..13271257,6	K562	blood:
5	chr6:13267359..13269532-chr6:13282342..13284920,2	MCF-7	breast:
6	chr6:13265469..13267865-chr6:13268622..13270348,2	K562	blood:

Variant related genes	Relation type
PHACTR1	TF binding region
ENSG00000215022	Chromatin interaction
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1014820	0.84[EUR][1000 genomes]
rs10948550	0.88[EUR][1000 genomes]
rs11751747	0.88[EUR][1000 genomes]
rs11755185	0.88[EUR][1000 genomes]
rs11963839	0.88[EUR][1000 genomes]
rs11966270	0.90[EUR][1000 genomes]
rs11967582	0.84[EUR][1000 genomes]
rs11968818	0.90[EUR][1000 genomes]
rs11969387	0.88[EUR][1000 genomes]
rs12525681	0.88[EUR][1000 genomes]
rs12525892	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12525906	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12527422	0.90[EUR][1000 genomes]
rs12527775	0.88[EUR][1000 genomes]
rs12528951	0.88[EUR][1000 genomes]
rs12528966	0.88[EUR][1000 genomes]
rs12660341	0.88[EUR][1000 genomes]
rs12660392	0.88[EUR][1000 genomes]
rs12660606	0.90[EUR][1000 genomes]
rs12661071	0.88[EUR][1000 genomes]
rs12665408	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12665414	0.84[EUR][1000 genomes]
rs12665416	0.84[EUR][1000 genomes]
rs1569418	0.84[EUR][1000 genomes]
rs1736501	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1736502	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs175729	0.90[EUR][1000 genomes]
rs17667989	0.87[AMR][1000 genomes]
rs1937765	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202024	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202026	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202031	0.87[AMR][1000 genomes]
rs202033	0.87[AMR][1000 genomes]
rs202037	0.87[AMR][1000 genomes]
rs202043	0.90[AMR][1000 genomes]
rs202049	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs202052	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202055	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202056	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202059	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs202061	0.90[EUR][1000 genomes]
rs202062	0.88[EUR][1000 genomes]
rs202063	0.88[EUR][1000 genomes]
rs202065	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs202076	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202078	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142568	0.88[EUR][1000 genomes]
rs34275015	0.88[EUR][1000 genomes]
rs364419	0.88[EUR][1000 genomes]
rs369946	0.87[AMR][1000 genomes]
rs377019	0.88[EUR][1000 genomes]
rs413167	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs417024	0.87[AMR][1000 genomes]
rs429919	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs429935	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs430216	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs434703	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs434923	0.87[AMR][1000 genomes]
rs436268	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs443150	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4711946	0.88[EUR][1000 genomes]
rs4711948	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4711949	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4711956	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4715154	0.84[EUR][1000 genomes]
rs4715155	0.84[EUR][1000 genomes]
rs4715157	0.84[EUR][1000 genomes]
rs4715158	0.84[EUR][1000 genomes]
rs4715159	0.84[EUR][1000 genomes]
rs4715168	0.93[EUR][1000 genomes]
rs4715174	0.88[EUR][1000 genomes]
rs4715183	0.88[EUR][1000 genomes]
rs4715184	0.88[EUR][1000 genomes]
rs533512	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs534449	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs555496	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58474010	0.84[EUR][1000 genomes]
rs59566077	0.84[EUR][1000 genomes]
rs602976	0.90[EUR][1000 genomes]
rs603394	0.88[EUR][1000 genomes]
rs644309	0.87[AMR][1000 genomes]
rs73355358	0.88[EUR][1000 genomes]
rs73355362	0.88[EUR][1000 genomes]
rs73355368	0.88[EUR][1000 genomes]
rs7765972	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs202075	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249200-13272200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
3	chr6:13256600-13272200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:13256600-13273200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:13256600-13278200	Weak transcription	Pancreas	Pancrea
6	chr6:13258800-13272200	Weak transcription	Left Ventricle	heart
7	chr6:13261400-13272200	Weak transcription	Brain Angular Gyrus	brain
8	chr6:13261400-13272200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:13261400-13273000	Weak transcription	Adipose Nuclei	Adipose
10	chr6:13261600-13272200	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:13262600-13272400	Enhancers	Primary B cells from peripheral blood	blood
12	chr6:13262600-13272800	Weak transcription	Primary T cells from cord blood	blood
13	chr6:13263400-13272400	Weak transcription	Spleen	Spleen
14	chr6:13264600-13272200	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:13267000-13269800	Weak transcription	Lung	lung
16	chr6:13267000-13274200	Weak transcription	Gastric	stomach
17	chr6:13267200-13272000	Enhancers	Primary B cells from cord blood	blood
18	chr6:13267400-13270400	Enhancers	Fetal Heart	heart
19	chr6:13267400-13272000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:13267400-13272200	Weak transcription	Brain Germinal Matrix	brain
21	chr6:13267400-13272200	Weak transcription	Fetal Stomach	stomach
22	chr6:13267400-13280400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
24	chr6:13267800-13272000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:13267800-13272200	Weak transcription	Brain Anterior Caudate	brain
26	chr6:13268000-13278800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:13268400-13272200	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr6:13268800-13269600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr6:13268800-13270400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:13268800-13270400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr6:13268800-13270400	Enhancers	Ovary	ovary
33	chr6:13268800-13270800	Enhancers	Primary hematopoietic stem cells	blood
34	chr6:13268800-13271000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:13269000-13269600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:13269000-13269600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:13269000-13269600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr6:13269000-13270000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:13269000-13270200	Enhancers	Placenta	Placenta
40	chr6:13269000-13270200	Enhancers	HSMM	muscle
41	chr6:13269000-13271200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr6:13269000-13272600	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr6:13269200-13269600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:13269200-13269600	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr6:13269200-13269600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr6:13269200-13269600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr6:13269200-13269600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr6:13269200-13269600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:13269200-13269600	Enhancers	HMEC	breast
50	chr6:13269200-13269600	Enhancers	K562	blood

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