Variant report

Variant	rs13328160
Chromosome Location	chr5:58572383-58572384
allele	C/T
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	SIN3A	chr5:58572307-58572488	H1-hESC	embryonic stem cell:	n/a	chr5:58572312-58572320
2	TCF12	chr5:58570995-58573403	A549	lung:	n/a	n/a
3	EP300	chr5:58571156-58572385	A549	lung:	n/a	chr5:58571497-58571511 chr5:58571638-58571652
4	POLR2A	chr5:58572113-58572532	SK-N-MC	brain:	n/a	n/a
5	GATA3	chr5:58571048-58573456	A549	lung:	n/a	chr5:58572097-58572107
6	REST	chr5:58571102-58572394	A549	lung:	n/a	chr5:58571726-58571739 chr5:58571372-58571385
7	POLR2A	chr5:58571211-58573626	Hela-S3	cervix:	n/a	n/a
8	SP1	chr5:58570680-58572402	A549	lung:	n/a	chr5:58572021-58572028
9	TBP	chr5:58571148-58573227	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:58570997-58573240	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:7052647..7053265-chr5:58571726..58572393,2	Hela-S3	cervix:
2	chr17:59327949..59328466-chr5:58571972..58572886,2	Hela-S3	cervix:

Variant related genes	Relation type
PDE4D	TF binding region
ENSG00000238923	Chromatin interaction
ENSG00000111678	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10036406	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10038599	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10055446	0.80[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs10056754	1.00[LWK][hapmap]
rs10059709	1.00[ASW][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap]
rs10060200	0.81[CEU][hapmap]
rs10061600	0.83[ASN][1000 genomes]
rs10061786	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10062176	1.00[LWK][hapmap]
rs10064893	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.87[ASN][1000 genomes]
rs10068836	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10070294	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10070436	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs10075364	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10440630	0.89[CHB][hapmap]
rs11738043	1.00[ASW][hapmap]
rs11740402	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap]
rs11747413	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13328175	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13328226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13356883	1.00[ASW][hapmap]
rs17444059	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17528257	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs17528285	1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.87[ASN][1000 genomes]
rs17528473	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17528634	0.91[CEU][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17724250	0.81[CEU][hapmap]
rs17780213	0.81[CEU][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap]
rs1824159	0.83[CEU][hapmap]
rs2112959	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28529077	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61683381	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6881054	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72765932	0.87[ASN][1000 genomes]
rs72765953	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72765961	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72765990	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9292201	0.91[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9292206	1.00[ASW][hapmap]
rs9686434	0.84[AMR][1000 genomes];0.93[EUR][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	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
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13328160	PHYHIP	trans	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58568200-58572800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr5:58568200-58572800	Active TSS	Stomach Smooth Muscle	stomach
3	chr5:58568600-58572400	Active TSS	Fetal Muscle Leg	muscle
4	chr5:58568600-58572600	Active TSS	Hela-S3	cervix
5	chr5:58569200-58572400	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr5:58570000-58572400	Active TSS	Right Atrium	heart
7	chr5:58570200-58572400	Active TSS	Duodenum Mucosa	Duodenum
8	chr5:58570200-58572400	Active TSS	Fetal Intestine Small	intestine
9	chr5:58570600-58572600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:58570800-58572400	Active TSS	Osteobl	bone
11	chr5:58571000-58573800	Enhancers	Fetal Heart	heart
12	chr5:58571200-58572400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:58571400-58572400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:58571400-58572400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr5:58571600-58572400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:58571600-58572400	Flanking Active TSS	HUVEC	blood vessel
17	chr5:58571600-58572400	Active TSS	NH-A	brain
18	chr5:58571600-58572600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:58571800-58572400	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr5:58571800-58572400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:58571800-58572400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:58571800-58572400	Weak transcription	Stomach Mucosa	stomach
23	chr5:58571800-58572600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:58571800-58579400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:58572000-58572400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr5:58572000-58572400	Active TSS	Primary hematopoietic stem cells	blood
27	chr5:58572000-58572400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr5:58572000-58572400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr5:58572000-58572400	Enhancers	Brain Angular Gyrus	brain
30	chr5:58572000-58572800	Weak transcription	Colonic Mucosa	Colon
31	chr5:58572000-58572800	Flanking Active TSS	Fetal Kidney	kidney
32	chr5:58572000-58572800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:58572000-58572800	Weak transcription	Right Ventricle	heart
34	chr5:58572000-58572800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:58572000-58573000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr5:58572000-58573000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr5:58572000-58573200	Enhancers	Brain Germinal Matrix	brain
38	chr5:58572000-58573400	Enhancers	Colon Smooth Muscle	Colon
39	chr5:58572000-58573600	Enhancers	Fetal Brain Male	brain
40	chr5:58572000-58573800	Enhancers	Placenta Amnion	Placenta Amnion
41	chr5:58572000-58582800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:58572200-58572400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr5:58572200-58572400	Enhancers	Primary B cells from cord blood	blood
44	chr5:58572200-58572400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:58572200-58572400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr5:58572200-58572400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr5:58572200-58572400	Enhancers	Psoas Muscle	Psoas
48	chr5:58572200-58572400	Flanking Active TSS	HMEC	breast
49	chr5:58572200-58572400	Flanking Active TSS	NHEK	skin
50	chr5:58572200-58572400	Enhancers	NHLF	lung

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