Variant report

Variant	rs2049300
Chromosome Location	chr3:47642726-47642727
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47603181..47605657-chr3:47642567..47645013,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1014228	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130139	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130143	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11130144	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11130145	0.81[AFR][1000 genomes]
rs11130146	0.80[AFR][1000 genomes]
rs11716582	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11929303	0.85[EUR][1000 genomes]
rs12489865	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12492915	0.88[AFR][1000 genomes]
rs12498027	0.82[AFR][1000 genomes]
rs12636198	0.83[EUR][1000 genomes]
rs12636863	0.81[AFR][1000 genomes]
rs13081356	0.82[AFR][1000 genomes]
rs13085978	0.86[EUR][1000 genomes]
rs1403578	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1403579	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1464614	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2140335	0.80[AFR][1000 genomes]
rs2280567	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293226	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34616865	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36033865	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3732530	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3755637	0.81[EUR][1000 genomes]
rs3755638	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs3772403	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4274776	0.98[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4858801	0.98[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4858803	0.82[AFR][1000 genomes]
rs4858842	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4858846	0.83[AFR][1000 genomes]
rs56746603	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs60322343	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61620099	0.98[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs61675361	0.85[EUR][1000 genomes]
rs6774170	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7613934	0.85[AFR][1000 genomes]
rs7621236	0.87[AFR][1000 genomes]
rs7624474	0.87[AFR][1000 genomes]
rs7631950	0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs868255	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs869508	0.81[EUR][1000 genomes]
rs870622	0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs883661	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs883662	0.83[EUR][1000 genomes]
rs883663	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1835200	chr3:47642233-47654375	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2049300	NME6	cis	Esophagus Muscularis	GTEx
rs2049300	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs2049300	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs2049300	ZNF589	cis	Nerve Tibial	GTEx
rs2049300	MRPS18AP1	cis	Nerve Tibial	GTEx
rs2049300	DHX30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47621000-47651600	Weak transcription	Right Atrium	heart
2	chr3:47621000-47653400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:47622600-47653400	Weak transcription	Stomach Mucosa	stomach
4	chr3:47623400-47655000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:47624000-47653200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:47625400-47651400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:47625600-47651200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:47626200-47698600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:47626400-47655600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:47626400-47680600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:47626600-47688600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:47626600-47699800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:47626800-47680800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr3:47631000-47650000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:47631200-47650200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:47631400-47644200	Weak transcription	Psoas Muscle	Psoas
17	chr3:47632000-47648800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:47632200-47645400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:47632200-47647200	Weak transcription	HUVEC	blood vessel
20	chr3:47632200-47648400	Weak transcription	NHDF-Ad	bronchial
21	chr3:47632200-47649200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:47632200-47649800	Weak transcription	Colonic Mucosa	Colon
23	chr3:47632200-47651200	Weak transcription	Right Ventricle	heart
24	chr3:47632400-47646800	Weak transcription	Ovary	ovary
25	chr3:47632400-47651400	Weak transcription	Gastric	stomach
26	chr3:47632400-47651400	Weak transcription	Pancreas	Pancrea
27	chr3:47632400-47652800	Weak transcription	Aorta	Aorta
28	chr3:47632400-47658600	Weak transcription	A549	lung
29	chr3:47632400-47660800	Weak transcription	Esophagus	oesophagus
30	chr3:47632600-47643400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:47632600-47648400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:47632800-47644200	Weak transcription	Fetal Kidney	kidney
33	chr3:47632800-47649800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr3:47632800-47650000	Weak transcription	NHLF	lung
35	chr3:47633200-47645400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:47633200-47645800	Weak transcription	Fetal Heart	heart
37	chr3:47633800-47643200	Strong transcription	GM12878-XiMat	blood
38	chr3:47634200-47661000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr3:47634400-47645200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:47634600-47645200	Strong transcription	Fetal Stomach	stomach
41	chr3:47635000-47651400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:47635000-47686800	Strong transcription	Dnd41	blood
43	chr3:47636000-47649200	Weak transcription	HMEC	breast
44	chr3:47636400-47647800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:47636600-47642800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:47636600-47645000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:47636600-47645000	Weak transcription	Fetal Lung	lung
48	chr3:47636600-47646800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:47636600-47647800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:47636600-47649000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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