Variant report

Variant	rs1366907
Chromosome Location	chr4:152682749-152682750
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	POLR2A	chr4:152681580-152682760	Raji	blood:	n/a	n/a
2	MTA3	chr4:152681834-152682834	GM12878	blood:	n/a	n/a
3	ATF1	chr4:152682038-152682763	K562	blood:	n/a	n/a
4	ESRRA	chr4:152681352-152683331	GM12878	blood:	n/a	chr4:152682488-152682498 chr4:152682488-152682498 chr4:152682484-152682500 chr4:152683015-152683031 chr4:152682487-152682500 chr4:152682488-152682500
5	RAD21	chr4:152682203-152682783	HepG2	liver:	n/a	n/a
6	MXI1	chr4:152681644-152682783	IMR90	lung:	n/a	n/a
7	SREBP1	chr4:152680936-152683044	GM12878	blood:	n/a	chr4:152682153-152682162 chr4:152682153-152682162
8	MXI1	chr4:152681285-152682910	SK-N-SH	brain:	n/a	n/a
9	HCFC1	chr4:152681492-152682932	Hela-S3	cervix:	n/a	n/a
10	SMC3	chr4:152682006-152683044	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:152681211-152682918	PBDE	blood:	n/a	n/a
12	CBX3	chr4:152681967-152682811	K562	blood:	n/a	n/a
13	MTA3	chr4:152681661-152682819	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:152681397-152682759	GM12891	blood:	n/a	n/a
15	CTCF	chr4:152681957-152682788	K562	blood:	n/a	n/a
16	JUN	chr4:152681410-152682812	K562	blood:	n/a	chr4:152682157-152682167 chr4:152682158-152682166 chr4:152682482-152682491 chr4:152682157-152682167 chr4:152682157-152682167
17	GABPA	chr4:152681413-152682774	MCF-7	breast:	n/a	n/a
18	RCOR1	chr4:152681743-152682826	GM12878	blood:	n/a	n/a
19	POLR2A	chr4:152681116-152682928	MCF10A-Er-Src	breast:	n/a	n/a
20	TBP	chr4:152681973-152682829	GM12878	blood:	n/a	n/a
21	CTCF	chr4:152682600-152682750	HA-sp	spinal cord:	n/a	n/a

Variant related genes	Relation type
PET112	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10001603	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10013612	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10016160	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10222838	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10222925	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099828	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11099829	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11723227	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12331037	0.85[GIH][hapmap]
rs12502446	0.90[ASN][1000 genomes]
rs12503677	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12506000	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12641433	0.96[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12641438	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12641441	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12647420	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12647462	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12647465	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12647616	0.86[EUR][1000 genomes]
rs13108359	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13119490	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13121178	0.80[EUR][1000 genomes]
rs13121190	0.84[EUR][1000 genomes]
rs13139327	0.85[EUR][1000 genomes]
rs13145446	0.80[EUR][1000 genomes]
rs13147021	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1397683	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1429558	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1429559	1.00[ASW][hapmap];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17360475	0.85[GIH][hapmap]
rs1877185	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877186	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877188	0.88[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2007218	0.83[GIH][hapmap]
rs2089811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2175409	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303866	0.94[JPT][hapmap]
rs2406973	0.96[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2406974	0.82[EUR][1000 genomes]
rs28659854	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3749561	0.81[GIH][hapmap]
rs3792691	0.83[GIH][hapmap]
rs3805356	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4399967	0.85[EUR][1000 genomes]
rs4554052	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4643789	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4696106	0.84[EUR][1000 genomes]
rs4696107	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4696108	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4696109	0.85[GIH][hapmap]
rs4696110	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696286	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4696287	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4696290	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696293	0.81[GIH][hapmap]
rs4696295	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696296	0.81[ASN][1000 genomes]
rs4696297	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58751443	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59350867	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61308159	0.85[EUR][1000 genomes]
rs6535816	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6535818	0.85[GIH][hapmap]
rs6535819	0.85[GIH][hapmap]
rs6535822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816002	0.82[EUR][1000 genomes]
rs6847844	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6849111	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6855883	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6857073	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654294	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669465	0.96[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7669761	0.96[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7669977	0.85[GIH][hapmap]
rs7675818	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867800	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996320	0.88[EUR][1000 genomes];0.88[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	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
2	nsv4552	chr4:152681211-152702457	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv964732	chr4:152682015-152696175	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1366907	PET112L	cis	cerebellum	SCAN
rs1366907	PET112L	cis	lymphoblastoid	seeQTL
rs1366907	FAM160A1	cis	cerebellum	SCAN
rs1366907	PET112L	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152681000-152683000	Active TSS	HepG2	liver
2	chr4:152681200-152682800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:152681200-152682800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:152681200-152682800	Active TSS	Fetal Brain Female	brain
5	chr4:152681200-152682800	Active TSS	Psoas Muscle	Psoas
6	chr4:152681200-152682800	Active TSS	NHDF-Ad	bronchial
7	chr4:152681200-152682800	Active TSS	NHLF	lung
8	chr4:152681400-152682800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:152681400-152682800	Active TSS	Fetal Muscle Trunk	muscle
10	chr4:152681400-152682800	Active TSS	Pancreas	Pancrea
11	chr4:152681600-152682800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:152681600-152682800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:152681600-152682800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr4:152681600-152682800	Active TSS	Cortex derived primary cultured neurospheres	brain
15	chr4:152681600-152682800	Active TSS	Aorta	Aorta
16	chr4:152681600-152682800	Active TSS	Colonic Mucosa	Colon
17	chr4:152681600-152682800	Active TSS	Fetal Kidney	kidney
18	chr4:152681600-152683000	Active TSS	Brain Cingulate Gyrus	brain
19	chr4:152681800-152682800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:152681800-152682800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:152681800-152682800	Active TSS	Ovary	ovary
22	chr4:152681800-152682800	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr4:152681800-152682800	Active TSS	Stomach Smooth Muscle	stomach
24	chr4:152681800-152683000	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr4:152682000-152682800	Active TSS	Placenta	Placenta
26	chr4:152682200-152682800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:152682200-152682800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:152682200-152682800	Enhancers	Stomach Mucosa	stomach
29	chr4:152682400-152682800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
30	chr4:152682400-152682800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:152682400-152682800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr4:152682400-152682800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr4:152682400-152682800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr4:152682400-152682800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr4:152682400-152682800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr4:152682400-152682800	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr4:152682400-152682800	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr4:152682400-152682800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr4:152682400-152682800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr4:152682400-152682800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr4:152682400-152682800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr4:152682400-152682800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr4:152682400-152682800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr4:152682400-152682800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr4:152682400-152682800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr4:152682400-152682800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:152682400-152682800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr4:152682400-152682800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:152682400-152682800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:152682400-152682800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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