Variant report

Variant	rs2112959
Chromosome Location	chr5:58569284-58569285
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10036406	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs10038599	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10041021	0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs10055446	1.00[CHB][hapmap]
rs10056754	1.00[LWK][hapmap]
rs10059709	0.88[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap]
rs10061786	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10062176	1.00[LWK][hapmap]
rs10064893	1.00[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap]
rs10068836	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];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10070436	1.00[CHB][hapmap]
rs10075364	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10440630	0.89[CHB][hapmap]
rs11740402	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	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]
rs13328175	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13328226	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]
rs13360907	0.88[ASN][1000 genomes]
rs17444059	1.00[ASW][hapmap];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];1.00[TSI][hapmap];0.96[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	0.85[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];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17528634	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17780213	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs28529077	0.96[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	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6881054	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72765942	0.88[ASN][1000 genomes]
rs72765953	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72765961	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72765990	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9292201	0.82[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs9686434	0.88[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
rs2112959	PHYHIP	trans	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58560400-58570000	Weak transcription	Fetal Lung	lung
2	chr5:58561000-58569800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:58561000-58571000	Weak transcription	Left Ventricle	heart
4	chr5:58565200-58571000	Weak transcription	Fetal Heart	heart
5	chr5:58567400-58572200	Active TSS	A549	lung
6	chr5:58567600-58570800	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr5:58568200-58572000	Active TSS	Colon Smooth Muscle	Colon
8	chr5:58568200-58572800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr5:58568200-58572800	Active TSS	Stomach Smooth Muscle	stomach
10	chr5:58568400-58572000	Active TSS	Rectal Smooth Muscle	rectum
11	chr5:58568600-58570600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:58568600-58571600	Active TSS	Fetal Kidney	kidney
13	chr5:58568600-58572200	Active TSS	Fetal Muscle Trunk	muscle
14	chr5:58568600-58572400	Active TSS	Fetal Muscle Leg	muscle
15	chr5:58568600-58572600	Active TSS	Hela-S3	cervix
16	chr5:58568800-58569400	Enhancers	Fetal Intestine Small	intestine
17	chr5:58568800-58569400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr5:58568800-58569800	Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr5:58568800-58571600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:58569000-58570200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:58569000-58572200	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr5:58569000-58572200	Active TSS	Fetal Intestine Large	intestine
23	chr5:58569200-58569800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:58569200-58570000	Active TSS	Primary hematopoietic stem cells	blood
25	chr5:58569200-58570000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:58569200-58570000	Weak transcription	Colonic Mucosa	Colon
27	chr5:58569200-58570000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:58569200-58570000	Weak transcription	Psoas Muscle	Psoas
29	chr5:58569200-58570000	Weak transcription	Right Atrium	heart
30	chr5:58569200-58570200	Active TSS	HUVEC	blood vessel
31	chr5:58569200-58572200	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr5:58569200-58572400	Active TSS	Rectal Mucosa Donor 31	rectum

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