Variant report

Variant	rs13139327
Chromosome Location	chr4:152728590-152728591
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10013612	0.85[EUR][1000 genomes]
rs10016160	0.85[EUR][1000 genomes]
rs10222838	0.85[EUR][1000 genomes]
rs10222925	0.85[EUR][1000 genomes]
rs11099828	0.89[EUR][1000 genomes]
rs11099829	0.90[EUR][1000 genomes]
rs11723227	0.85[EUR][1000 genomes]
rs11943626	0.80[ASN][1000 genomes]
rs11944921	0.96[ASN][1000 genomes]
rs12502446	0.82[EUR][1000 genomes]
rs12641433	0.96[CEU][hapmap];0.90[TSI][hapmap]
rs13108359	0.96[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13119490	0.84[EUR][1000 genomes]
rs13121178	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13121190	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13136369	0.90[ASN][1000 genomes]
rs13145446	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13147021	0.88[EUR][1000 genomes]
rs1366907	1.00[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs1397683	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1429558	0.85[EUR][1000 genomes]
rs1429559	1.00[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs1877185	0.85[EUR][1000 genomes]
rs1877186	0.85[EUR][1000 genomes]
rs1877188	0.88[CEU][hapmap]
rs2089811	0.80[ASW][hapmap];1.00[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2175409	0.85[EUR][1000 genomes]
rs2406973	0.96[CEU][hapmap];0.90[TSI][hapmap]
rs34359168	0.80[ASN][1000 genomes]
rs34615528	0.80[ASN][1000 genomes]
rs3762906	0.80[YRI][hapmap]
rs3805356	1.00[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs3828546	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4279186	0.80[ASN][1000 genomes]
rs4399967	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4525955	0.80[ASN][1000 genomes]
rs4554052	0.90[EUR][1000 genomes]
rs4643789	0.94[EUR][1000 genomes]
rs4696110	0.83[EUR][1000 genomes]
rs4696290	0.96[CEU][hapmap];0.90[TSI][hapmap]
rs4696295	0.96[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4696297	0.88[EUR][1000 genomes]
rs56175637	0.80[ASN][1000 genomes]
rs58751443	0.86[EUR][1000 genomes]
rs59350867	0.85[EUR][1000 genomes]
rs61308159	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6535816	0.96[CEU][hapmap]
rs6535822	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6816292	0.99[ASN][1000 genomes]
rs6836954	0.80[ASN][1000 genomes]
rs6846809	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6847303	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6847844	0.85[EUR][1000 genomes]
rs6849111	0.86[EUR][1000 genomes]
rs6855883	0.84[EUR][1000 genomes]
rs6857073	0.85[EUR][1000 genomes]
rs7438281	0.80[YRI][hapmap]
rs7654294	0.85[EUR][1000 genomes]
rs7669465	0.96[CEU][hapmap];0.90[TSI][hapmap]
rs7669761	0.96[CEU][hapmap];0.90[TSI][hapmap]
rs7675818	0.85[EUR][1000 genomes]
rs867800	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13139327	PET112L	cis	cerebellum	SCAN
rs13139327	PET112L	cis	parietal	SCAN
rs13139327	FAM160A1	cis	cerebellum	SCAN
rs13139327	PET112L	cis	multi-tissue	Pritchard

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152720200-152728600	Weak transcription	Right Atrium	heart
2	chr4:152721000-152729000	Weak transcription	Left Ventricle	heart
3	chr4:152721200-152729200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:152721200-152731400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:152723600-152729000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:152723800-152729200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:152724000-152729800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:152725000-152728600	Enhancers	HSMM	muscle
9	chr4:152726000-152731800	Enhancers	Fetal Heart	heart
10	chr4:152726200-152731200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:152726400-152732000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:152726800-152730000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:152727200-152729400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr4:152727200-152730000	Enhancers	HSMMtube	muscle
15	chr4:152727400-152728800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:152727400-152729200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr4:152727400-152729400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:152727400-152729600	Enhancers	NHDF-Ad	bronchial
19	chr4:152727400-152729800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr4:152727400-152729800	Enhancers	NHEK	skin
21	chr4:152727400-152729800	Enhancers	Osteobl	bone
22	chr4:152727600-152728600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:152727600-152728600	Enhancers	Placenta	Placenta
24	chr4:152727600-152728800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr4:152727600-152728800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:152727600-152728800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr4:152727600-152728800	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr4:152727600-152729000	Enhancers	Adipose Nuclei	Adipose
29	chr4:152727600-152729400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:152727600-152729400	Enhancers	Stomach Smooth Muscle	stomach
31	chr4:152727600-152729800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:152727800-152728600	Enhancers	Aorta	Aorta
33	chr4:152727800-152728800	Enhancers	Fetal Intestine Large	intestine
34	chr4:152727800-152729200	Enhancers	Fetal Intestine Small	intestine
35	chr4:152727800-152729400	Enhancers	Fetal Muscle Leg	muscle
36	chr4:152727800-152729400	Enhancers	NHLF	lung
37	chr4:152728000-152728800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:152728000-152729400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:152728200-152729200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr4:152728200-152732000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr4:152728200-152732000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:152728400-152728800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr4:152728400-152729400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:152728400-152729400	Enhancers	Duodenum Mucosa	Duodenum
45	chr4:152728400-152729400	Enhancers	Fetal Muscle Trunk	muscle
46	chr4:152728400-152729400	Enhancers	NH-A	brain
47	chr4:152728400-152729600	Flanking Active TSS	Hela-S3	cervix
48	chr4:152728400-152729800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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