Variant report

Variant	rs2406973
Chromosome Location	chr4:152608339-152608340
allele	A/C
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	GATA3	chr4:152608011-152608970	SK-N-SH	brain:	n/a	n/a
2	RXRA	chr4:152608302-152608888	SK-N-SH	brain:	n/a	chr4:152608552-152608566 chr4:152608541-152608557
3	GATA3	chr4:152608200-152608537	SH-SY5Y	brain:	n/a	n/a
4	GATA3	chr4:152608077-152608957	SK-N-SH	brain:	n/a	n/a
5	GATA2	chr4:152608034-152608753	SH-SY5Y	brain:	n/a	n/a
6	GATA3	chr4:152608104-152608701	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
PET112	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10001603	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10013612	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10016160	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10019048	0.82[GIH][hapmap]
rs10222838	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10222925	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11723227	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12503677	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12641433	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641438	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641441	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647420	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647462	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647465	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647616	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13119490	0.80[EUR][1000 genomes]
rs1366907	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]
rs1397683	0.92[CEU][hapmap]
rs1429558	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1429559	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]
rs1877185	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1877186	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1877188	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1896883	0.82[GIH][hapmap]
rs2089811	0.96[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2175409	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2278304	0.82[GIH][hapmap]
rs2406974	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2840130	0.82[GIH][hapmap];0.82[MEX][hapmap]
rs28659854	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805356	0.96[CEU][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs3828546	0.96[CEU][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4571	0.80[GIH][hapmap]
rs4696106	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696107	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696108	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696110	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4696286	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696287	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696290	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4696295	0.92[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs58751443	0.85[EUR][1000 genomes]
rs59350867	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6535816	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6535822	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6810860	0.82[GIH][hapmap]
rs6816002	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6833368	0.82[GIH][hapmap]
rs6834095	0.82[GIH][hapmap]
rs6838966	0.82[GIH][hapmap]
rs6839074	0.82[GIH][hapmap]
rs6840360	0.82[GIH][hapmap]
rs6840678	0.80[GIH][hapmap]
rs6847844	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6849050	0.82[GIH][hapmap]
rs6849111	0.85[EUR][1000 genomes]
rs6855883	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6857073	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7439465	0.82[GIH][hapmap]
rs7654294	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7669465	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669761	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7675818	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs867800	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9996320	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	esv2755535	chr4:152549395-152609395	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv4551	chr4:152582617-152627367	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1026511	chr4:152593382-152611915	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2406973	PET112L	cis	parietal	SCAN
rs2406973	PET112L	cis	lymphoblastoid	seeQTL
rs2406973	PET112L	cis	Lymphoblastoid	GTEx
rs2406973	PET112L	cis	multi-tissue	Pritchard
rs2406973	PET112L	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152563800-152625200	Weak transcription	Hela-S3	cervix
2	chr4:152567400-152608600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:152567800-152609000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:152581200-152608400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr4:152585600-152628600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:152585800-152640400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:152586400-152609000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:152589200-152608800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:152589200-152619200	Weak transcription	Dnd41	blood
10	chr4:152590600-152609000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr4:152591200-152608600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr4:152591200-152646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:152592600-152636400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:152593600-152608800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:152595200-152611600	Weak transcription	K562	blood
16	chr4:152595600-152608600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:152596200-152608600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:152596200-152624000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:152596400-152608600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:152596400-152608600	Weak transcription	Placenta	Placenta
21	chr4:152596400-152609000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:152596400-152627800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:152596400-152628600	Weak transcription	Colonic Mucosa	Colon
24	chr4:152596400-152640600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:152596600-152608600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:152596800-152608800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr4:152597000-152608400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:152597000-152612000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:152597200-152608400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:152597200-152608800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:152597400-152609200	Weak transcription	Fetal Brain Female	brain
32	chr4:152598000-152612000	Weak transcription	Brain Germinal Matrix	brain
33	chr4:152598200-152608600	Weak transcription	NHDF-Ad	bronchial
34	chr4:152598200-152609400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:152598200-152609600	Weak transcription	NHLF	lung
36	chr4:152598400-152648200	Weak transcription	HMEC	breast
37	chr4:152598800-152620800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:152599000-152637200	Weak transcription	GM12878-XiMat	blood
39	chr4:152600600-152626200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr4:152600800-152608600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:152601200-152608800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr4:152601200-152612000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:152603000-152623200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:152603400-152608400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr4:152603600-152610600	Strong transcription	Fetal Intestine Small	intestine
46	chr4:152604800-152608400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:152604800-152620600	Weak transcription	Pancreas	Pancrea
48	chr4:152605000-152608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr4:152605200-152608800	Weak transcription	Fetal Intestine Large	intestine
50	chr4:152605400-152609000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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