Variant report

Variant	rs6472225
Chromosome Location	chr8:66753261-66753262
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	HA-E2F1	chr8:66753029-66754975	Hela-S3	cervix:	n/a	chr8:66753923-66753935 chr8:66754804-66754813 chr8:66754343-66754352 chr8:66754043-66754052 chr8:66754345-66754354 chr8:66754563-66754572 chr8:66753852-66753861 chr8:66754806-66754815 chr8:66754010-66754020 chr8:66753589-66753599
2	POLR2A	chr8:66753252-66753264	MCF-7	breast:	n/a	n/a
3	RCOR1	chr8:66752882-66753690	K562	blood:	n/a	n/a
4	CEBPB	chr8:66753113-66753398	K562	blood:	n/a	n/a
5	POLR2A	chr8:66753002-66753277	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr8:66752331-66755723	GM12878	blood:	n/a	n/a
7	RUNX3	chr8:66752830-66753345	GM12878	blood:	n/a	n/a
8	CTCF	chr8:66753120-66753270	NHDF-neo	bronchial:	n/a	n/a
9	ZBTB7A	chr8:66752999-66753758	ECC-1	luminal epithelium:	n/a	n/a
10	TFAP2A	chr8:66752947-66755267	Hela-S3	cervix:	n/a	chr8:66753360-66753372 chr8:66754901-66754909 chr8:66754900-66754908 chr8:66753154-66753165 chr8:66754900-66754908 chr8:66753586-66753597 chr8:66754049-66754060 chr8:66754901-66754909 chr8:66754917-66754929 chr8:66753917-66753929 chr8:66753814-66753829 chr8:66754049-66754060 chr8:66754049-66754060 chr8:66754900-66754908 chr8:66754918-66754926 chr8:66754898-66754913 chr8:66754049-66754060 chr8:66754044-66754059 chr8:66754901-66754909
11	TFAP2C	chr8:66752921-66755242	Hela-S3	cervix:	n/a	chr8:66753977-66753992
12	MAZ	chr8:66753021-66755211	Hela-S3	cervix:	n/a	chr8:66753804-66753814
13	E2F6	chr8:66753026-66753265	K562	blood:	n/a	n/a
14	POLR2A	chr8:66753009-66755120	NB4	blood:	n/a	n/a
15	ZBTB7A	chr8:66752990-66753946	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr8:66753076-66753741	GM12878	blood:	n/a	n/a
17	MAX	chr8:66752882-66755371	A549	lung:	n/a	chr8:66753804-66753814
18	TEAD4	chr8:66753054-66753403	H1-hESC	embryonic stem cell:	n/a	n/a
19	TCF7L2	chr8:66753034-66755019	HCT-116	colon:	n/a	n/a
20	CHD1	chr8:66752809-66753719	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr8:66753160-66753310	GM12872	blood:	n/a	n/a
22	SMC3	chr8:66752962-66753278	Hela-S3	cervix:	n/a	n/a
23	TAF7	chr8:66752996-66753832	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr8:66752959-66753831	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr8:66752942-66755373	Hela-S3	cervix:	n/a	n/a
26	SIN3A	chr8:66752852-66755413	H1-hESC	embryonic stem cell:	n/a	chr8:66753844-66753855
27	GTF2F1	chr8:66753047-66753663	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr8:66753120-66753270	HCFaa	heart:	n/a	n/a
29	POLR2A	chr8:66752993-66753411	GM12878	blood:	n/a	n/a
30	CTCF	chr8:66753066-66753278	GM12892	blood:	n/a	n/a
31	MAX	chr8:66752957-66753298	K562	blood:	n/a	n/a
32	CTBP2	chr8:66753011-66753709	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr8:66752897-66753331	MCF10A-Er-Src	breast:	n/a	n/a
34	ZEB1	chr8:66752926-66753443	GM12878	blood:	n/a	chr8:66753225-66753234 chr8:66753249-66753260
35	POLR2A	chr8:66753067-66755091	MCF-7	breast:	n/a	n/a
36	POLR2A	chr8:66752955-66755115	GM15510	blood:	n/a	n/a
37	E2F4	chr8:66752943-66753322	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr8:66752970-66755143	GM12878	blood:	n/a	n/a
39	MXI1	chr8:66752908-66753906	Hela-S3	cervix:	n/a	n/a
40	IRF1	chr8:66752731-66753280	K562	blood:	n/a	chr8:66753003-66753017 chr8:66752814-66752830 chr8:66753003-66753015
41	STAT5A	chr8:66752421-66753786	GM12878	blood:	n/a	chr8:66753018-66753026 chr8:66753440-66753448
42	POLR2A	chr8:66752760-66755625	GM12892	blood:	n/a	n/a
43	UBTF	chr8:66752860-66755031	K562	blood:	n/a	n/a
44	POLR2A	chr8:66752610-66755499	GM12878	blood:	n/a	n/a
45	MYC	chr8:66753027-66755138	NB4	blood:	n/a	chr8:66753804-66753814
46	BHLHE40	chr8:66753080-66753280	K562	blood:	n/a	chr8:66753160-66753176
47	POLR2A	chr8:66752928-66755640	GM12892	blood:	n/a	n/a
48	POLR2A	chr8:66752904-66755510	PBDE	blood:	n/a	n/a
49	POLR2A	chr8:66753070-66753298	HepG2	liver:	n/a	n/a
50	CTCF	chr8:66753180-66753330	GM12864	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:66753039..66754980-chr8:67343764..67346186,2	K562	blood:
2	chr8:66695473..66703733-chr8:66751774..66756006,10	K562	blood:
3	chr8:66752746..66756404-chr8:66931747..66936511,11	MCF-7	breast:
4	chr8:66752587..66755352-chr8:66933051..66936501,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272192	TF binding region
PDE7A	TF binding region
ENSG00000147576	Chromatin interaction
ENSG00000205268	Chromatin interaction
ENSG00000147570	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11782766	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1316700	0.81[GIH][hapmap]
rs1513723	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs16932346	0.90[JPT][hapmap]
rs1877640	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2063685	0.89[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28501341	1.00[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs56139500	0.85[ASN][1000 genomes]
rs57463822	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6415604	0.90[JPT][hapmap]
rs6472222	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[YRI][hapmap];0.90[ASN][1000 genomes]
rs6472226	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6472227	0.81[JPT][hapmap]
rs67441920	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7014676	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[ASN][1000 genomes]
rs7828699	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7829484	0.81[JPT][hapmap]
rs972362	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs974149	0.84[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][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	esv1793412	chr8:66705321-66761366	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv3446467	chr8:66749863-67667068	Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3325067	chr8:66753023-66755571	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6472225	DNAJC5B	cis	lymphoblastoid	seeQTL
rs6472225	PDE7A	cis	parietal	SCAN
rs6472225	MTFR1	cis	cerebellum	SCAN
rs6472225	MTFR1	cis	parietal	SCAN
rs6472225	EPHB1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:66748000-66754600	Active TSS	Primary T cells fromperipheralblood	blood
2	chr8:66748200-66755800	Active TSS	Thymus	Thymus
3	chr8:66749200-66755200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr8:66749600-66755000	Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr8:66749600-66755000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
6	chr8:66749800-66755000	Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr8:66750000-66753400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr8:66750200-66754400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr8:66750800-66755000	Active TSS	GM12878-XiMat	blood
10	chr8:66751000-66755200	Active TSS	Right Atrium	heart
11	chr8:66751000-66755600	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr8:66751200-66754400	Active TSS	HMEC	breast
13	chr8:66751200-66754800	Active TSS	Fetal Thymus	thymus
14	chr8:66751200-66755200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr8:66751200-66755200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr8:66751200-66755200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:66751200-66755400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr8:66751400-66755000	Active TSS	Dnd41	blood
19	chr8:66751400-66755800	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr8:66751800-66755000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr8:66751800-66755200	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr8:66751800-66755200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr8:66751800-66755200	Active TSS	K562	blood
24	chr8:66751800-66755400	Active TSS	NHDF-Ad	bronchial
25	chr8:66752000-66755000	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr8:66752000-66755000	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr8:66752000-66755000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr8:66752000-66755000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr8:66752000-66755000	Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr8:66752000-66755000	Active TSS	Hela-S3	cervix
31	chr8:66752000-66755000	Active TSS	NHLF	lung
32	chr8:66752000-66755200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr8:66752000-66755400	Active TSS	H1 Cell Line	embryonic stem cell
34	chr8:66752000-66755400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr8:66752200-66753600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr8:66752200-66753800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr8:66752200-66754000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
38	chr8:66752200-66754800	Active TSS	NHEK	skin
39	chr8:66752200-66755000	Active TSS	Primary T cells from cord blood	blood
40	chr8:66752200-66755000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr8:66752200-66755000	Active TSS	A549	lung
42	chr8:66752200-66755200	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr8:66752200-66755600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr8:66752400-66753400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr8:66752400-66753400	Flanking Active TSS	HUVEC	blood vessel
46	chr8:66752400-66755000	Active TSS	Brain Angular Gyrus	brain
47	chr8:66752400-66755200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr8:66752400-66755200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr8:66752400-66755200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr8:66752400-66755200	Active TSS	Fetal Kidney	kidney

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