Variant report

Variant	rs13085978
Chromosome Location	chr3:47650075-47650076
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	POLR2A	chr3:47649619-47650216	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47649126..47651542-chr3:47653050..47654614,2	K562	blood:
2	chr3:47644023..47648902-chr3:47649054..47653658,7	K562	blood:

Variant related genes	Relation type
ENSG00000214773	TF binding region
ENSG00000214773	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1014228	0.96[EUR][1000 genomes]
rs10865948	0.92[EUR][1000 genomes]
rs11130138	0.87[EUR][1000 genomes]
rs11130139	0.92[EUR][1000 genomes]
rs11130143	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11130144	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11130145	0.86[EUR][1000 genomes]
rs11130146	0.84[EUR][1000 genomes]
rs11707707	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11712152	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11712464	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11716582	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11927129	0.89[AMR][1000 genomes]
rs11929303	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489865	0.83[EUR][1000 genomes]
rs12492915	0.93[EUR][1000 genomes]
rs12497921	0.85[EUR][1000 genomes]
rs12498027	0.87[EUR][1000 genomes]
rs12633604	0.82[EUR][1000 genomes]
rs12635438	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12636198	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12636863	0.90[EUR][1000 genomes]
rs13061412	0.86[EUR][1000 genomes]
rs13063042	0.82[EUR][1000 genomes]
rs13069142	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13081356	0.86[EUR][1000 genomes]
rs13084555	0.84[EUR][1000 genomes]
rs1403578	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1403579	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1464614	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049300	0.86[EUR][1000 genomes]
rs2049301	0.82[EUR][1000 genomes]
rs2133601	0.81[EUR][1000 genomes]
rs2140335	0.84[EUR][1000 genomes]
rs2280567	0.93[EUR][1000 genomes]
rs2293226	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2882611	0.86[EUR][1000 genomes]
rs34252990	0.92[EUR][1000 genomes]
rs34616865	0.97[EUR][1000 genomes]
rs35167544	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35664069	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36033865	0.82[EUR][1000 genomes]
rs3732530	0.93[EUR][1000 genomes]
rs3755637	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3755638	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3772403	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4274776	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858801	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858836	0.86[EUR][1000 genomes]
rs4858842	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858846	0.87[EUR][1000 genomes]
rs4858853	0.89[AMR][1000 genomes]
rs4858863	0.83[AMR][1000 genomes]
rs55823596	0.89[AMR][1000 genomes]
rs56376646	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56746603	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60110914	0.92[EUR][1000 genomes]
rs60322343	0.93[EUR][1000 genomes]
rs61620099	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61675361	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262084	0.87[AFR][1000 genomes]
rs62263561	0.89[AMR][1000 genomes]
rs6442072	0.93[EUR][1000 genomes]
rs6442074	0.82[EUR][1000 genomes]
rs6442086	0.89[AMR][1000 genomes]
rs6772301	0.82[EUR][1000 genomes]
rs6773467	0.82[EUR][1000 genomes]
rs6773732	0.82[EUR][1000 genomes]
rs6774170	0.96[EUR][1000 genomes]
rs6776963	0.90[AMR][1000 genomes]
rs6784946	0.83[EUR][1000 genomes]
rs6785031	0.84[EUR][1000 genomes]
rs6789835	0.86[EUR][1000 genomes]
rs73085151	0.89[AMR][1000 genomes]
rs7429162	0.82[EUR][1000 genomes]
rs7613934	0.93[EUR][1000 genomes]
rs7621236	0.93[EUR][1000 genomes]
rs7624474	0.93[EUR][1000 genomes]
rs7629850	0.83[AMR][1000 genomes]
rs7631950	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7642691	0.86[EUR][1000 genomes]
rs868255	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs869508	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs870622	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883661	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883662	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883663	0.96[EUR][1000 genomes];0.89[ASN][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13085978	MRPS18AP1	cis	Artery Tibial	GTEx
rs13085978	MRPS18AP1	cis	lung	GTEx
rs13085978	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs13085978	NME6	cis	Esophagus Muscularis	GTEx
rs13085978	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs13085978	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs13085978	MRPS18AP1	cis	Nerve Tibial	GTEx
rs13085978	ZNF589	cis	Nerve Tibial	GTEx

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	chr3:47631200-47650200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:47632200-47651200	Weak transcription	Right Ventricle	heart
16	chr3:47632400-47651400	Weak transcription	Gastric	stomach
17	chr3:47632400-47651400	Weak transcription	Pancreas	Pancrea
18	chr3:47632400-47652800	Weak transcription	Aorta	Aorta
19	chr3:47632400-47658600	Weak transcription	A549	lung
20	chr3:47632400-47660800	Weak transcription	Esophagus	oesophagus
21	chr3:47634200-47661000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:47635000-47651400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:47635000-47686800	Strong transcription	Dnd41	blood
24	chr3:47636800-47651400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:47636800-47672800	Weak transcription	Small Intestine	intestine
26	chr3:47637200-47665000	Strong transcription	Primary T cells from cord blood	blood
27	chr3:47638000-47681200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:47638200-47665800	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:47638800-47651400	Strong transcription	Fetal Muscle Leg	muscle
30	chr3:47639000-47652600	Strong transcription	Fetal Intestine Large	intestine
31	chr3:47639200-47653600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:47639200-47654600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:47639200-47655000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr3:47639200-47655200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:47639200-47655200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:47639200-47655600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:47639200-47675800	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:47640000-47651400	Weak transcription	Spleen	Spleen
39	chr3:47641800-47655800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:47642800-47653600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:47643600-47653600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:47643600-47684800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:47643800-47650200	Weak transcription	Fetal Brain Male	brain
44	chr3:47643800-47651400	Weak transcription	Brain Substantia Nigra	brain
45	chr3:47643800-47666400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:47644000-47654000	Strong transcription	Fetal Thymus	thymus
47	chr3:47644200-47652400	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:47644200-47676000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:47644400-47654200	Strong transcription	Primary B cells from cord blood	blood
50	chr3:47644400-47655200	Strong transcription	GM12878-XiMat	blood

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