Variant report

Variant	rs1867725
Chromosome Location	chr5:58513701-58513702
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	CTCF	chr5:58513689-58513769	Medullo	brain:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17443688	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2216699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56334860	0.80[EUR][1000 genomes]
rs59019685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61584344	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450513	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66589198	0.92[EUR][1000 genomes]
rs67123835	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67272153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67656226	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6867240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867591	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872782	0.89[ASN][1000 genomes]
rs72765910	1.00[EUR][1000 genomes]
rs72765918	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs974766	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1023570	chr5:58486384-58537849	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58474400-58520000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:58485000-58518800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:58485600-58518200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:58490400-58519200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:58491400-58515600	Weak transcription	Fetal Stomach	stomach
6	chr5:58496200-58515600	Weak transcription	Fetal Kidney	kidney
7	chr5:58502000-58517200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:58503200-58514400	Weak transcription	HUVEC	blood vessel
9	chr5:58506400-58518200	Weak transcription	Left Ventricle	heart
10	chr5:58506400-58520400	Weak transcription	Stomach Mucosa	stomach
11	chr5:58509200-58518400	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:58509400-58518800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:58510000-58515600	Weak transcription	Psoas Muscle	Psoas
14	chr5:58510200-58517800	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:58510400-58520000	Weak transcription	Right Ventricle	heart
16	chr5:58510800-58515600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:58511000-58515400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:58511000-58515800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:58511400-58515600	Weak transcription	Fetal Heart	heart
20	chr5:58511800-58521600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr5:58512000-58516200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:58512200-58514000	Enhancers	Colon Smooth Muscle	Colon
23	chr5:58512200-58514000	Enhancers	Fetal Intestine Large	intestine
24	chr5:58512400-58514200	Enhancers	Fetal Intestine Small	intestine
25	chr5:58512600-58514000	Weak transcription	Fetal Brain Male	brain
26	chr5:58512800-58518200	Weak transcription	Gastric	stomach
27	chr5:58512800-58518200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:58512800-58532400	Weak transcription	Pancreas	Pancrea
29	chr5:58513000-58514000	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr5:58513000-58517800	Weak transcription	Hela-S3	cervix
31	chr5:58513200-58513800	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr5:58513200-58514000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr5:58513400-58513800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:58513400-58513800	Enhancers	Duodenum Mucosa	Duodenum
35	chr5:58513400-58514000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:58513600-58513800	Transcr. at gene 5' and 3'	A549	lung
37	chr5:58513600-58514000	Enhancers	Fetal Lung	lung
38	chr5:58513600-58514400	Enhancers	Duodenum Smooth Muscle	Duodenum

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