Variant report

Variant	rs2878298
Chromosome Location	chr3:49406080-49406081
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	SP1	chr3:49405767-49406126	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
RHOA-IT1	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1050450	0.94[ASN][1000 genomes]
rs10865955	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130192	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130193	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11130194	0.88[EUR][1000 genomes]
rs11130196	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11130199	0.83[EUR][1000 genomes]
rs11711536	0.94[ASN][1000 genomes]
rs11716974	0.82[ASN][1000 genomes]
rs13086611	0.94[ASN][1000 genomes]
rs13087851	0.94[ASN][1000 genomes]
rs13090388	0.94[ASN][1000 genomes]
rs13096760	0.90[EUR][1000 genomes]
rs1464566	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464567	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1464568	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568661	0.83[EUR][1000 genomes]
rs1568662	0.82[EUR][1000 genomes]
rs17080528	0.94[ASN][1000 genomes]
rs17595772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650792	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800668	0.94[ASN][1000 genomes]
rs1987628	0.94[ASN][1000 genomes]
rs2117939	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34588335	0.94[ASN][1000 genomes]
rs34937635	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35169793	0.94[ASN][1000 genomes]
rs35701831	0.83[EUR][1000 genomes]
rs3811699	0.94[ASN][1000 genomes]
rs3877784	0.83[EUR][1000 genomes]
rs3924462	0.83[EUR][1000 genomes]
rs4459909	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4563439	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4855842	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4855843	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4855859	0.83[EUR][1000 genomes]
rs4855861	0.81[EUR][1000 genomes]
rs4855864	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4855866	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855873	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855877	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4955412	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955438	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55957735	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59152804	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62259939	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62259942	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6446264	0.94[ASN][1000 genomes]
rs6446274	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67485053	0.88[ASN][1000 genomes]
rs6773518	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6784820	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6792911	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793308	0.94[ASN][1000 genomes]
rs6797765	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809216	0.94[ASN][1000 genomes]
rs7371895	0.81[EUR][1000 genomes]
rs7373849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623659	0.94[ASN][1000 genomes]
rs7631908	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7637999	0.83[EUR][1000 genomes]
rs7643586	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7643845	0.82[EUR][1000 genomes]
rs7645445	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7648841	0.94[ASN][1000 genomes]
rs885592	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2878298	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs2878298	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs2878298	WDR6	cis	Artery Tibial	GTEx
rs2878298	WDR6	cis	lung	GTEx
rs2878298	WDR6	cis	Adipose Subcutaneous	GTEx
rs2878298	WDR6	cis	Nerve Tibial	GTEx
rs2878298	WDR6	cis	Muscle Skeletal	GTEx
rs2878298	WDR6	cis	Whole Blood	GTEx
rs2878298	AMT	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49396400-49413600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:49396400-49418600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49396600-49406200	Strong transcription	Rectal Smooth Muscle	rectum
4	chr3:49396600-49410200	Weak transcription	Psoas Muscle	Psoas
5	chr3:49396600-49413200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:49396600-49413200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr3:49396600-49413800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr3:49396600-49414400	Weak transcription	Fetal Brain Male	brain
9	chr3:49396800-49406200	Strong transcription	Stomach Smooth Muscle	stomach
10	chr3:49396800-49408000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr3:49396800-49410800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:49396800-49412800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:49396800-49413200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:49396800-49413400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:49396800-49413400	Strong transcription	Thymus	Thymus
16	chr3:49396800-49413600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:49396800-49438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:49397000-49406200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:49397000-49406400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:49397000-49408000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:49397000-49412800	Strong transcription	Lung	lung
22	chr3:49397000-49413000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:49397000-49413200	Strong transcription	Adipose Nuclei	Adipose
24	chr3:49397000-49415200	Strong transcription	Fetal Stomach	stomach
25	chr3:49397200-49406400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:49397200-49413400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:49397200-49423800	Weak transcription	Fetal Heart	heart
28	chr3:49397400-49410400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:49397400-49410600	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:49397400-49411200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:49397400-49413200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:49397400-49413200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:49397400-49413400	Strong transcription	Fetal Intestine Large	intestine
34	chr3:49397400-49413400	Strong transcription	Fetal Muscle Leg	muscle
35	chr3:49397400-49413400	Strong transcription	Placenta	Placenta
36	chr3:49397400-49416400	Strong transcription	Fetal Intestine Small	intestine
37	chr3:49397600-49413200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:49397600-49413200	Strong transcription	Spleen	Spleen
39	chr3:49397600-49413600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:49397800-49406200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:49397800-49409000	Weak transcription	Fetal Kidney	kidney
42	chr3:49397800-49413200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:49397800-49413600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:49397800-49413800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:49397800-49415800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:49398800-49410600	Weak transcription	Small Intestine	intestine
47	chr3:49399000-49448000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:49400600-49413200	Strong transcription	Primary T cells from cord blood	blood
49	chr3:49400800-49413600	Strong transcription	Fetal Thymus	thymus
50	chr3:49401200-49406200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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