Variant report

Variant	rs6472226
Chromosome Location	chr8:66755163-66755164
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	MAX	chr8:66753891-66755421	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr8:66753774-66755321	U87	brain:	n/a	n/a
3	ATF2	chr8:66754052-66755317	GM12878	blood:	n/a	chr8:66754802-66754816 chr8:66754840-66754851 chr8:66754343-66754354 chr8:66754804-66754815 chr8:66754341-66754355
4	POLR2A	chr8:66753527-66755170	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr8:66753965-66755313	U87	brain:	n/a	n/a
6	POLR2A	chr8:66753965-66755368	U87	brain:	n/a	n/a
7	E2F4	chr8:66754034-66755227	MCF10A-Er-Src	breast:	n/a	chr8:66754804-66754813 chr8:66754343-66754352 chr8:66754043-66754052 chr8:66754345-66754354 chr8:66754563-66754572 chr8:66754806-66754815
8	POLR2A	chr8:66752331-66755723	GM12878	blood:	n/a	n/a
9	POLR2A	chr8:66753531-66755251	K562	blood:	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	IRF1	chr8:66754104-66755435	K562	blood:	n/a	chr8:66755099-66755113 chr8:66754922-66754936
13	SMC3	chr8:66754042-66755355	GM12878	blood:	n/a	chr8:66754161-66754171
14	MAZ	chr8:66753021-66755211	Hela-S3	cervix:	n/a	chr8:66753804-66753814
15	CTCF	chr8:66755160-66755310	SK-N-SH_RA	brain:	n/a	chr8:66755278-66755287
16	USF2	chr8:66755020-66755307	Hela-S3	cervix:	n/a	n/a
17	CHD2	chr8:66754218-66755184	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr8:66752882-66755371	A549	lung:	n/a	chr8:66753804-66753814
19	PML	chr8:66753886-66755531	GM12878	blood:	n/a	n/a
20	POLR2A	chr8:66753979-66755255	HepG2	liver:	n/a	n/a
21	MAFK	chr8:66753992-66755274	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr8:66753988-66755252	HUVEC	blood vessel:	n/a	n/a
23	YY1	chr8:66754153-66755164	H1-hESC	embryonic stem cell:	n/a	chr8:66754328-66754339 chr8:66754241-66754252
24	POLR2A	chr8:66752942-66755373	Hela-S3	cervix:	n/a	n/a
25	STAT5A	chr8:66754368-66755464	GM12878	blood:	n/a	chr8:66755101-66755112
26	MXI1	chr8:66753536-66755206	GM12878	blood:	n/a	chr8:66754830-66754845
27	SIN3A	chr8:66752852-66755413	H1-hESC	embryonic stem cell:	n/a	chr8:66753844-66753855
28	SIN3A	chr8:66754235-66755300	GM12878	blood:	n/a	n/a
29	ATF2	chr8:66754204-66755384	GM12878	blood:	n/a	chr8:66754802-66754816 chr8:66754840-66754851 chr8:66754343-66754354 chr8:66754804-66754815 chr8:66754341-66754355
30	ZNF143	chr8:66754232-66755283	H1-hESC	embryonic stem cell:	n/a	chr8:66754240-66754258 chr8:66754269-66754279
31	TEAD4	chr8:66754059-66755447	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr8:66753868-66755169	SK-N-MC	brain:	n/a	n/a
33	POLR2A	chr8:66753437-66755296	K562	blood:	n/a	n/a
34	TBL1XR1	chr8:66754145-66755428	GM12878	blood:	n/a	n/a
35	CREB1	chr8:66753829-66755384	GM12878	blood:	n/a	chr8:66754803-66754816 chr8:66754342-66754355
36	POLR2A	chr8:66753892-66755379	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr8:66755140-66755290	HPAF	blood vessel:	n/a	chr8:66755278-66755287
38	BHLHE40	chr8:66753963-66755283	GM12878	blood:	n/a	n/a
39	ZNF143	chr8:66753618-66755399	GM12878	blood:	n/a	chr8:66754240-66754258 chr8:66754269-66754279
40	POLR2A	chr8:66753837-66755171	H1-hESC	embryonic stem cell:	n/a	n/a
41	RUNX3	chr8:66754058-66755197	GM12878	blood:	n/a	n/a
42	GATA3	chr8:66753951-66755181	A549	lung:	n/a	n/a
43	REST	chr8:66754103-66755446	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr8:66753829-66755545	HL-60	blood:	n/a	n/a
45	POLR2A	chr8:66752760-66755625	GM12892	blood:	n/a	n/a
46	TCF12	chr8:66753958-66755600	ECC-1	luminal epithelium:	n/a	n/a
47	RELA	chr8:66754044-66755391	GM18505	blood:	n/a	n/a
48	POLR2A	chr8:66752610-66755499	GM12878	blood:	n/a	n/a
49	POLR2A	chr8:66754220-66755505	GM12891	blood:	n/a	n/a
50	POLR2A	chr8:66753857-66755215	Gliobla	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:66755120-66755170	SKMC	muscle:	n/a
2	chr8:66755120-66755170	SK-N-MC	brain:	n/a
3	chr8:66755120-66755170	ProgFib	skin:	n/a
4	chr8:66755120-66755170	AG04450	lung:	fetal
5	chr8:66755120-66755170	PFSK-1	brain:	n/a
6	chr8:66755120-66755170	HCF	heart:	n/a
7	chr8:66755120-66755170	GM19239	blood:	n/a
8	chr8:66755120-66755170	HCPEpiC	choroid plexus:	n/a
9	chr8:66755120-66755170	AG10803	skin:	n/a
10	chr8:66755120-66755170	HRPEpiC	eye:	n/a
11	chr8:66755120-66755170	RPTEC	kidney:	n/a
12	chr8:66755120-66755170	HRCEpiC	kidney:	n/a
13	chr8:66755120-66755170	SAEC	small airway:	n/a
14	chr8:66755120-66755170	GM12892	blood:	n/a
15	chr8:66755120-66755170	K562	blood:	n/a
16	chr8:66755120-66755170	HRE	kidney:	n/a
17	chr8:66755120-66755170	SK-N-SH_RA	brain:	n/a
18	chr8:66755120-66755170	LNCaP	prostate:	n/a
19	chr8:66755120-66755170	MCF10A-Er-Src	breast:	n/a
20	chr8:66755120-66755170	Hepatocyte	liver:	n/a
21	chr8:66755120-66755170	T-47D	breast:	n/a
22	chr8:66755120-66755170	NB4	blood:	n/a
23	chr8:66755120-66755170	IMR90	lung:	fetal
24	chr8:66755120-66755170	U87	brain:	n/a
25	chr8:66755120-66755170	NHDF-neo	bronchial:	n/a
26	chr8:66755120-66755170	Caco-2	colon:	n/a
27	chr8:66755120-66755170	HAEpiC	amniotic membrane:	n/a
28	chr8:66755120-66755170	CMK	blood:	n/a
29	chr8:66755120-66755170	HIPEpiC	eye:	n/a
30	chr8:66755120-66755170	HEEpiC	esophagus:	n/a
31	chr8:66755120-66755170	HCM	heart:	n/a
32	chr8:66755120-66755170	PrEC	prostate:	n/a
33	chr8:66755120-66755170	HUVEC	blood vessel:	n/a
34	chr8:66755120-66755170	NT2-D1	testis:	n/a
35	chr8:66755120-66755170	GM12891	blood:	n/a
36	chr8:66755120-66755170	HMEC	breast:	n/a
37	chr8:66755120-66755170	AG09309	skin:	n/a
38	chr8:66755120-66755170	A549	lung:	n/a
39	chr8:66755120-66755170	HPAEpiC	pulmonary alveolar:	n/a
40	chr8:66755120-66755170	PANC-1	pancreas:	n/a
41	chr8:66755120-66755170	Jurkat	blood:	n/a
42	chr8:66755120-66755170	AG04449	skin:	fetal
43	chr8:66755120-66755170	NHBE	bronchial:	n/a
44	chr8:66755120-66755170	HEK293	kidney:	embryo
45	chr8:66755120-66755170	AoSMC	blood vessel:	n/a
46	chr8:66755120-66755170	H1-hESC	embryonic stem cell:	embryo
47	chr8:66755120-66755170	BJ	skin:	n/a
48	chr8:66755120-66755170	Hela-S3	cervix:	n/a
49	chr8:66755120-66755170	HNPCEpiC	eye:	n/a
50	chr8:66755120-66755170	HL-60	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:66754330..66755269-chr9:140135296..140136144,2	HCT-116	colon:
2	chr8:66695473..66703733-chr8:66751774..66756006,10	K562	blood:
3	chr8:66754751..66755294-chr9:131580425..131581265,2	NB4	blood:
4	chr8:66755086..66757057-chr8:66757170..66760034,2	MCF-7	breast:
5	chr8:66752746..66756404-chr8:66931747..66936511,11	MCF-7	breast:
6	chr6:42017972..42018535-chr8:66754653..66755319,2	NB4	blood:
7	chr8:66752587..66755352-chr8:66933051..66936501,7	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTFR1-1	chr8:66754987-66755566	ENSG00000272192.1

Variant related genes	Relation type
PDE7A	TF binding region
PDE7A	CpG island
ENSG00000137413	Chromatin interaction
ENSG00000205268	Chromatin interaction
ENSG00000147570	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000167136	Chromatin interaction
ENSG00000112576	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11782766	0.89[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1316700	0.88[GIH][hapmap]
rs1513723	0.85[CEU][hapmap]
rs16932346	0.81[JPT][hapmap]
rs1877640	0.93[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2063685	0.89[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs28501341	0.85[ASW][hapmap];0.83[CEU][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap]
rs56139500	0.83[ASN][1000 genomes]
rs57463822	0.87[ASN][1000 genomes]
rs6415604	0.82[JPT][hapmap]
rs6472222	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.88[YRI][hapmap];0.88[ASN][1000 genomes]
rs6472225	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	0.91[JPT][hapmap]
rs67441920	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7014676	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs7828699	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7829484	0.91[JPT][hapmap]
rs972362	0.93[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs974149	0.93[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6472226	PDE7A	cis	parietal	SCAN
rs6472226	MTFR1	cis	cerebellum	SCAN
rs6472226	DNAJC5B	cis	lymphoblastoid	seeQTL
rs6472226	MTFR1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:66748200-66755800	Active TSS	Thymus	Thymus
2	chr8:66749200-66755200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr8:66751000-66755200	Active TSS	Right Atrium	heart
4	chr8:66751000-66755600	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr8:66751200-66755200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:66751200-66755200	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr8:66751200-66755200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr8:66751200-66755400	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr8:66751400-66755800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr8:66751800-66755200	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr8:66751800-66755200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr8:66751800-66755200	Active TSS	K562	blood
13	chr8:66751800-66755400	Active TSS	NHDF-Ad	bronchial
14	chr8:66752000-66755200	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr8:66752000-66755400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr8:66752000-66755400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr8:66752200-66755200	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr8:66752200-66755600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr8:66752400-66755200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr8:66752400-66755200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr8:66752400-66755200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr8:66752400-66755200	Active TSS	Fetal Kidney	kidney
23	chr8:66752400-66755200	Active TSS	Fetal Muscle Leg	muscle
24	chr8:66752400-66755400	Active TSS	H9 Cell Line	embryonic stem cell
25	chr8:66752400-66755600	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr8:66752600-66755200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:66752600-66755200	Active TSS	Fetal Stomach	stomach
28	chr8:66752600-66755200	Active TSS	Left Ventricle	heart
29	chr8:66752600-66755200	Active TSS	Pancreas	Pancrea
30	chr8:66752600-66755200	Active TSS	Right Ventricle	heart
31	chr8:66752600-66755200	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr8:66752600-66755200	Active TSS	HSMM	muscle
33	chr8:66752600-66755400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr8:66752600-66755400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr8:66752600-66755400	Active TSS	Small Intestine	intestine
36	chr8:66752800-66755200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:66752800-66755200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr8:66752800-66755200	Active TSS	Brain Hippocampus Middle	brain
39	chr8:66752800-66755200	Active TSS	Fetal Brain Female	brain
40	chr8:66752800-66755200	Active TSS	Ovary	ovary
41	chr8:66752800-66755200	Active TSS	Psoas Muscle	Psoas
42	chr8:66752800-66755200	Active TSS	Stomach Mucosa	stomach
43	chr8:66752800-66755400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr8:66752800-66755600	Active TSS	Fetal Brain Male	brain
45	chr8:66753000-66755200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr8:66753000-66755200	Active TSS	Aorta	Aorta
47	chr8:66753000-66755200	Active TSS	Brain Cingulate Gyrus	brain
48	chr8:66753000-66755200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr8:66753000-66755200	Active TSS	Brain Substantia Nigra	brain
50	chr8:66753000-66755200	Active TSS	Duodenum Mucosa	Duodenum

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