Variant report

Variant	rs12047517
Chromosome Location	chr1:79305991-79305992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:79299275..79301209-chr1:79305174..79307511,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12024487	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12562487	0.80[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs12568976	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs1489387	0.80[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs1489401	0.80[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap]
rs17102310	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17102369	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs17102395	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs1780753	0.82[ASN][1000 genomes]
rs1780754	0.82[ASN][1000 genomes]
rs1780755	0.82[ASN][1000 genomes]
rs1780762	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41322946	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4650615	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs931413	0.82[ASN][1000 genomes]
rs931414	0.82[ASN][1000 genomes]
rs931415	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs971064	0.80[CEU][hapmap];0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv491784	chr1:79146141-79853482	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv526221	chr1:79197624-79487080	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv817535	chr1:79203834-79473089	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999624	chr1:79230028-79448222	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535013	chr1:79230028-79448222	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv546619	chr1:79233493-79614989	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1000656	chr1:79303750-79337233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1003295	chr1:79303750-79344930	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12047517	PTGFR	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79302800-79306000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:79302800-79306200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:79302800-79306200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:79303000-79306000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:79303000-79306000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:79303000-79306200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:79305600-79306200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:79305600-79306200	Enhancers	Muscle Satellite Cultured Cells	--
9	chr1:79305600-79306200	Enhancers	Fetal Lung	lung
10	chr1:79305600-79306200	Enhancers	HSMM	muscle
11	chr1:79305600-79306200	Enhancers	NHDF-Ad	bronchial
12	chr1:79305600-79306200	Enhancers	Osteobl	bone
13	chr1:79305600-79306400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr1:79305600-79307400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:79305800-79306200	Enhancers	Liver	Liver
16	chr1:79305800-79306200	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr1:79305800-79306200	Enhancers	NH-A	brain
18	chr1:79305800-79306400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:79305800-79306600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:79305800-79307600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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