Variant report

Variant	rs3749293
Chromosome Location	chr3:157261335-157261336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12485399	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12492543	0.86[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12493333	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12494755	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12498099	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16827792	0.85[ASN][1000 genomes]
rs16827862	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2034093	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2083818	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680380	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57157485	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60734635	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60849513	0.85[AMR][1000 genomes]
rs62278667	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766351	0.86[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6783699	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6795972	0.89[ASN][1000 genomes]
rs6798962	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6804345	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3749293	C3orf55	cis	parietal	SCAN
rs3749293	VEPH1	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157260400-157261400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr3:157260400-157261400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
3	chr3:157260400-157261400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:157260400-157261600	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr3:157260400-157261600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:157260400-157261600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:157260400-157261600	Active TSS	Colon Smooth Muscle	Colon
8	chr3:157260400-157261600	Active TSS	Fetal Brain Female	brain
9	chr3:157260400-157261600	Active TSS	A549	lung
10	chr3:157260400-157261600	Active TSS	HSMM	muscle
11	chr3:157260400-157261800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
12	chr3:157260400-157262000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:157260400-157262200	Active TSS	NHLF	lung
14	chr3:157260600-157261400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
15	chr3:157260600-157261400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:157260600-157261400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:157260600-157261400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:157260600-157261400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:157260600-157261400	Active TSS	Duodenum Mucosa	Duodenum
20	chr3:157260600-157261400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
21	chr3:157260600-157261400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
22	chr3:157260600-157261400	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr3:157260600-157261400	Flanking Bivalent TSS/Enh	Placenta	Placenta
24	chr3:157260600-157261400	Active TSS	Ovary	ovary
25	chr3:157260600-157261400	Active TSS	Pancreas	Pancrea
26	chr3:157260600-157261400	Active TSS	Placenta Amnion	Placenta Amnion
27	chr3:157260600-157261400	Active TSS	Stomach Mucosa	stomach
28	chr3:157260600-157261600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr3:157260600-157261600	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr3:157260600-157261600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr3:157260600-157261600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
32	chr3:157260600-157261600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr3:157260600-157261600	Active TSS	Brain Anterior Caudate	brain
34	chr3:157260600-157261600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
35	chr3:157260600-157261600	Active TSS	HSMMtube	muscle
36	chr3:157260600-157261600	Flanking Active TSS	HUVEC	blood vessel
37	chr3:157260600-157261800	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr3:157260600-157261800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:157260600-157261800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:157260600-157261800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:157260600-157261800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:157260600-157261800	Active TSS	Right Atrium	heart
43	chr3:157260600-157262000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:157260600-157262000	Active TSS	NHDF-Ad	bronchial
45	chr3:157260800-157261400	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr3:157260800-157261400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:157260800-157261400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:157260800-157261400	Active TSS	Aorta	Aorta
49	chr3:157260800-157261400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
50	chr3:157260800-157261400	Active TSS	Fetal Kidney	kidney

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