Variant report

Variant	rs13328226
Chromosome Location	chr5:58571915-58571916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000238923	Chromatin interaction
ENSG00000111678	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10036406	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs10038599	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10041021	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs10055446	0.80[CEU][hapmap];1.00[CHB][hapmap]
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]
rs10061786	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][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];1.00[LWK][hapmap]
rs10068836	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
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];0.90[ASN][1000 genomes]
rs10070436	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10075364	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][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];0.88[ASN][1000 genomes]
rs11747413	1.00[CHB][hapmap]
rs13328160	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]
rs13328175	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13356883	1.00[ASW][hapmap]
rs13360907	0.88[ASN][1000 genomes]
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];0.90[ASN][1000 genomes]
rs17528257	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs17528285	1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap]
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];0.90[ASN][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];1.00[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];1.00[ASN][1000 genomes]
rs28529077	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28647633	0.88[ASN][1000 genomes]
rs60453299	0.88[ASN][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];0.90[ASN][1000 genomes]
rs72765942	0.88[ASN][1000 genomes]
rs72765953	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72765961	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][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
rs13328226	PHYHIP	trans	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58567400-58572200	Active TSS	A549	lung
2	chr5:58568200-58572000	Active TSS	Colon Smooth Muscle	Colon
3	chr5:58568200-58572800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr5:58568200-58572800	Active TSS	Stomach Smooth Muscle	stomach
5	chr5:58568400-58572000	Active TSS	Rectal Smooth Muscle	rectum
6	chr5:58568600-58572200	Active TSS	Fetal Muscle Trunk	muscle
7	chr5:58568600-58572400	Active TSS	Fetal Muscle Leg	muscle
8	chr5:58568600-58572600	Active TSS	Hela-S3	cervix
9	chr5:58569000-58572200	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr5:58569000-58572200	Active TSS	Fetal Intestine Large	intestine
11	chr5:58569200-58572200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr5:58569200-58572400	Active TSS	Rectal Mucosa Donor 31	rectum
13	chr5:58569400-58572200	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr5:58569800-58572200	Active TSS	Fetal Stomach	stomach
15	chr5:58570000-58572000	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr5:58570000-58572000	Active TSS	Brain Angular Gyrus	brain
17	chr5:58570000-58572000	Active TSS	Colonic Mucosa	Colon
18	chr5:58570000-58572200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:58570000-58572200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:58570000-58572400	Active TSS	Right Atrium	heart
21	chr5:58570200-58572000	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr5:58570200-58572200	Active TSS	Brain Anterior Caudate	brain
23	chr5:58570200-58572200	Active TSS	Brain Hippocampus Middle	brain
24	chr5:58570200-58572400	Active TSS	Duodenum Mucosa	Duodenum
25	chr5:58570200-58572400	Active TSS	Fetal Intestine Small	intestine
26	chr5:58570600-58572200	Active TSS	Fetal Lung	lung
27	chr5:58570600-58572600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:58570800-58572000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr5:58570800-58572200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:58570800-58572200	Active TSS	Brain Substantia Nigra	brain
31	chr5:58570800-58572200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr5:58570800-58572200	Active TSS	HMEC	breast
33	chr5:58570800-58572400	Active TSS	Osteobl	bone
34	chr5:58571000-58572000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:58571000-58572000	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr5:58571000-58572000	Active TSS	Primary B cells from cord blood	blood
37	chr5:58571000-58572000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
38	chr5:58571000-58572000	Active TSS	Muscle Satellite Cultured Cells	--
39	chr5:58571000-58572000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:58571000-58572000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:58571000-58572000	Active TSS	Brain Cingulate Gyrus	brain
42	chr5:58571000-58572000	Active TSS	Ovary	ovary
43	chr5:58571000-58572000	Active TSS	Right Ventricle	heart
44	chr5:58571000-58572000	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr5:58571000-58572200	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr5:58571000-58572200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:58571000-58572200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr5:58571000-58572200	Active TSS	Aorta	Aorta
49	chr5:58571000-58572200	Active TSS	NHDF-Ad	bronchial
50	chr5:58571000-58573800	Enhancers	Fetal Heart	heart

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