Variant report

Variant	rs6679677
Chromosome Location	chr1:114303808-114303809
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:114303724-114303851	K562	blood:	n/a	n/a
2	POLR2A	chr1:114300923-114303939	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:114303443-114304049	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:114300980-114305965	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114301552..114304210-chr11:59521950..59524919,2	MCF-7	breast:
2	chr1:114301057..114304105-chr1:114310097..114314111,4	MCF-7	breast:
3	chr1:114298167..114305255-chr1:114351008..114356451,27	MCF-7	breast:
4	chr1:114302807..114305155-chr1:114318148..114320872,2	K562	blood:
5	chr1:114300422..114303875-chr1:114445198..114448512,7	MCF-7	breast:
6	chr1:114302426..114304248-chr1:114378191..114380113,2	MCF-7	breast:
7	chr1:114303734..114306910-chr1:114471256..114474152,4	MCF-7	breast:
8	chr1:114300189..114305139-chr20:48598182..48603040,8	MCF-7	breast:
9	chr1:114303634..114306529-chr1:114324305..114326913,3	K562	blood:
10	chr1:114303216..114304873-chr1:114343722..114346617,2	K562	blood:
11	chr1:114247347..114249870-chr1:114302601..114305068,2	MCF-7	breast:

No data

Variant related genes	Relation type
PHTF1	TF binding region
ENSG00000134262	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000166900	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000124216	Chromatin interaction
ENSG00000254477	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1230666	1.00[ASW][hapmap]
rs2476601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

Variant related diseases (count:7)

Disease	PMID	Source
Type 1 diabetes	17554300	GWAS catalog
Rheumatoid arthritis	17554300	GWAS catalog
Crohn's disease	23128233	GWAS catalog
Type 1 diabetes	18978792	GWAS catalog
Hypothyroidism	22493691	GWAS catalog
Rheumatoid arthritis	18794853	GWAS catalog
Type 1 diabetes	17554260	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6679677	PHTF1	cis	cerebellum	SCAN
rs6679677	MAGI3	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114302200-114304000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:114302400-114311800	Weak transcription	Small Intestine	intestine
3	chr1:114302600-114308600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:114302600-114308800	Weak transcription	Gastric	stomach
5	chr1:114302600-114309400	Weak transcription	Esophagus	oesophagus
6	chr1:114302600-114318000	Weak transcription	Spleen	Spleen
7	chr1:114302600-114321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:114302800-114306200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:114302800-114306200	Weak transcription	Placenta	Placenta
10	chr1:114302800-114306400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:114302800-114307400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:114302800-114307400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:114302800-114307400	Weak transcription	HSMM	muscle
14	chr1:114302800-114307600	Weak transcription	Primary T cells from cord blood	blood
15	chr1:114302800-114307600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:114302800-114307600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:114302800-114307600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr1:114302800-114307800	Weak transcription	Fetal Intestine Small	intestine
19	chr1:114302800-114308000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:114302800-114308000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:114302800-114308000	Weak transcription	Fetal Thymus	thymus
22	chr1:114302800-114308200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:114302800-114308400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:114302800-114308600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:114302800-114308600	Weak transcription	Left Ventricle	heart
26	chr1:114302800-114308600	Weak transcription	Lung	lung
27	chr1:114302800-114308600	Weak transcription	Ovary	ovary
28	chr1:114302800-114309400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:114302800-114310200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:114302800-114310600	Weak transcription	NHEK	skin
31	chr1:114302800-114311800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:114302800-114312200	Weak transcription	Stomach Mucosa	stomach
33	chr1:114302800-114315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:114302800-114323200	Weak transcription	Aorta	Aorta
35	chr1:114302800-114323600	Weak transcription	Psoas Muscle	Psoas
36	chr1:114302800-114326000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:114302800-114326200	Weak transcription	Pancreas	Pancrea
38	chr1:114302800-114326200	Weak transcription	Right Ventricle	heart
39	chr1:114303000-114304200	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr1:114303000-114305200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:114303000-114305800	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:114303000-114306000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:114303000-114306000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr1:114303000-114306000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:114303000-114306200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:114303000-114306400	Weak transcription	Fetal Brain Female	brain
47	chr1:114303000-114306400	Weak transcription	Fetal Kidney	kidney
48	chr1:114303000-114306800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:114303000-114307400	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:114303000-114307400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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