Variant report

Variant	rs2452009
Chromosome Location	chr4:95495908-95495909
allele	C/T
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	chr4:95495742-95496447	SK-N-SH	brain:	n/a	chr4:95496035-95496045
2	GATA3	chr4:95495760-95496373	SK-N-SH	brain:	n/a	chr4:95496035-95496045

Variant related genes	Relation type
PDLIM5	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12510147	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1493112	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2452578	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452597	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452598	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2452599	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2452600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2510770	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2510773	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3133150	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35044129	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4699540	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66542996	0.98[EUR][1000 genomes]
rs6845201	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7682375	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2452009	PDLIM5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95479800-95496800	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:95481400-95496800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:95481400-95496800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:95483400-95496600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:95483400-95496800	Weak transcription	NHEK	skin
6	chr4:95483400-95524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:95483600-95496200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:95483800-95496600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:95483800-95496800	Weak transcription	Gastric	stomach
10	chr4:95483800-95497000	Weak transcription	HMEC	breast
11	chr4:95484000-95496600	Weak transcription	HSMMtube	muscle
12	chr4:95484000-95507400	Weak transcription	Hela-S3	cervix
13	chr4:95484600-95496800	Weak transcription	HSMM	muscle
14	chr4:95485600-95496600	Weak transcription	Ovary	ovary
15	chr4:95485800-95496800	Weak transcription	Psoas Muscle	Psoas
16	chr4:95485800-95496800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:95486000-95496800	Weak transcription	Aorta	Aorta
18	chr4:95486800-95496600	Weak transcription	Right Ventricle	heart
19	chr4:95487000-95496600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:95489000-95496800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:95489000-95507400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:95489200-95496800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:95489200-95506800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr4:95489200-95507400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:95489200-95509800	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr4:95489400-95496600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:95489400-95496600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:95489400-95496800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:95489400-95496800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr4:95489400-95496800	Weak transcription	Adipose Nuclei	Adipose
31	chr4:95489400-95496800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:95489400-95496800	Weak transcription	Right Atrium	heart
33	chr4:95489400-95496800	Weak transcription	K562	blood
34	chr4:95489400-95506200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:95489600-95496800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:95489600-95508200	Weak transcription	GM12878-XiMat	blood
37	chr4:95489600-95522800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:95489600-95539200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:95490400-95496600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:95490600-95496800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:95491400-95496800	Weak transcription	Esophagus	oesophagus
42	chr4:95491800-95496800	Weak transcription	Fetal Kidney	kidney
43	chr4:95492000-95496600	Weak transcription	NHLF	lung
44	chr4:95492000-95496800	Weak transcription	Brain Germinal Matrix	brain
45	chr4:95492000-95496800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:95492000-95496800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:95492000-95496800	Weak transcription	Fetal Intestine Large	intestine
48	chr4:95492000-95502200	Weak transcription	Fetal Intestine Small	intestine
49	chr4:95492200-95496400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:95492200-95496800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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