Variant report

Variant	rs6472227
Chromosome Location	chr8:66755558-66755559
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	POLR2A	chr8:66752331-66755723	GM12878	blood:	n/a	n/a
2	POLR2A	chr8:66752760-66755625	GM12892	blood:	n/a	n/a
3	TCF12	chr8:66753958-66755600	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr8:66752928-66755640	GM12892	blood:	n/a	n/a
5	EP300	chr8:66753729-66755581	ECC-1	luminal epithelium:	n/a	chr8:66754995-66755009 chr8:66754270-66754279 chr8:66753941-66753950 chr8:66754271-66754287
6	POLR2A	chr8:66753222-66755618	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr8:66753878-66755572	SK-N-MC	brain:	n/a	n/a
8	HCFC1	chr8:66753870-66755596	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr8:66751976-66755639	SK-N-SH	brain:	n/a	chr8:66754830-66754845
10	POLR2A	chr8:66752832-66755573	HepG2	liver:	n/a	n/a
11	CREB1	chr8:66753940-66755603	GM12878	blood:	n/a	chr8:66754803-66754816 chr8:66754342-66754355
12	JUN	chr8:66753952-66755682	K562	blood:	n/a	chr8:66754344-66754353 chr8:66754805-66754814 chr8:66754804-66754817 chr8:66755239-66755253
13	POLR2A	chr8:66752753-66755770	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr8:66752577-66755734	H1-neurons	neurons:	n/a	chr8:66753801-66753814 chr8:66752614-66752623 chr8:66753166-66753176
15	SMC3	chr8:66754237-66755566	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr8:66752534-66755736	GM12891	blood:	n/a	n/a
17	TBP	chr8:66754138-66755634	GM12878	blood:	n/a	n/a
18	POLR2A	chr8:66753494-66755985	K562	blood:	n/a	n/a
19	KAP1	chr8:66754895-66755619	K562	blood:	n/a	n/a
20	TEAD4	chr8:66754065-66755597	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr8:66752920-66755611	H1-neurons	neurons:	n/a	n/a
22	ELK1	chr8:66754258-66755608	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:66695473..66703733-chr8:66751774..66756006,10	K562	blood:
2	chr8:66755086..66757057-chr8:66757170..66760034,2	MCF-7	breast:
3	chr8:66752746..66756404-chr8:66931747..66936511,11	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
ENSG00000147570	Chromatin interaction
ENSG00000205268	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11782766	0.81[JPT][hapmap]
rs16932346	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1877640	0.81[JPT][hapmap]
rs2063685	0.81[JPT][hapmap]
rs6415604	1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs6472222	0.81[JPT][hapmap]
rs6472225	0.81[JPT][hapmap]
rs6472226	0.91[JPT][hapmap]
rs7005571	1.00[CHB][hapmap]
rs7014676	0.81[JPT][hapmap]
rs73242909	0.88[ASN][1000 genomes]
rs73242913	0.94[ASN][1000 genomes]
rs7821744	1.00[CHB][hapmap]
rs7828699	0.81[JPT][hapmap]
rs7829484	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs972362	0.81[JPT][hapmap]
rs974149	0.81[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6472227	MTFR1	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:66748200-66755800	Active TSS	Thymus	Thymus
2	chr8:66751000-66755600	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr8:66751400-66755800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr8:66752200-66755600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr8:66752400-66755600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr8:66752800-66755600	Active TSS	Fetal Brain Male	brain
7	chr8:66753000-66755600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:66755000-66755600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr8:66755000-66755600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr8:66755000-66755600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr8:66755000-66755600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr8:66755000-66755600	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr8:66755000-66755600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr8:66755000-66755600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr8:66755000-66755600	Flanking Active TSS	Fetal Lung	lung
16	chr8:66755000-66755600	Flanking Active TSS	Dnd41	blood
17	chr8:66755000-66755600	Flanking Active TSS	GM12878-XiMat	blood
18	chr8:66755000-66755600	Flanking Active TSS	Hela-S3	cervix
19	chr8:66755000-66755600	Flanking Active TSS	Osteobl	bone
20	chr8:66755000-66755800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr8:66755000-66755800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr8:66755000-66756600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr8:66755000-66756600	Enhancers	HMEC	breast
24	chr8:66755200-66755600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr8:66755200-66755600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr8:66755200-66755600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr8:66755200-66755600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr8:66755200-66755600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr8:66755200-66755600	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr8:66755200-66755600	Flanking Active TSS	K562	blood
31	chr8:66755200-66755800	Flanking Active TSS	Fetal Kidney	kidney
32	chr8:66755400-66755600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr8:66755400-66755600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr8:66755400-66755600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr8:66755400-66755600	Enhancers	Primary B cells from cord blood	blood
36	chr8:66755400-66755600	Enhancers	Primary B cells from peripheral blood	blood
37	chr8:66755400-66755600	Enhancers	Primary hematopoietic stem cells	blood
38	chr8:66755400-66755600	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr8:66755400-66755600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr8:66755400-66755600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr8:66755400-66755600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr8:66755400-66755600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr8:66755400-66755600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr8:66755400-66755600	Active TSS	Muscle Satellite Cultured Cells	--
45	chr8:66755400-66755600	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr8:66755400-66755600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr8:66755400-66755600	Enhancers	Brain Angular Gyrus	brain
48	chr8:66755400-66755600	Enhancers	Brain Cingulate Gyrus	brain
49	chr8:66755400-66755600	Enhancers	Brain Germinal Matrix	brain
50	chr8:66755400-66755600	Enhancers	Colon Smooth Muscle	Colon

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