Variant report

Variant	rs62263561
Chromosome Location	chr3:47792785-47792786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47791204..47794202-chr3:47822128..47824852,3	MCF-7	breast:
2	chr3:47777066..47780209-chr3:47791992..47794562,3	K562	blood:
3	chr3:47792486..47796208-chr3:47820472..47824381,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173473	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs11130145	0.80[EUR][1000 genomes]
rs11130146	0.80[EUR][1000 genomes]
rs11130147	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11130148	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130150	0.87[EUR][1000 genomes]
rs11707707	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11708849	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11710199	0.84[EUR][1000 genomes]
rs11712152	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11712464	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714942	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11927129	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11929303	0.87[AMR][1000 genomes]
rs12495204	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12633604	0.80[EUR][1000 genomes]
rs12635438	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12636198	0.87[AMR][1000 genomes]
rs13061412	0.80[EUR][1000 genomes]
rs13063042	0.85[EUR][1000 genomes]
rs13064183	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13069142	0.86[AMR][1000 genomes]
rs13070035	0.92[EUR][1000 genomes]
rs13077230	0.87[EUR][1000 genomes]
rs13079407	0.82[EUR][1000 genomes]
rs13081356	0.80[EUR][1000 genomes]
rs13085978	0.89[AMR][1000 genomes]
rs13086149	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13091913	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13094264	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13098128	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13319205	0.86[EUR][1000 genomes]
rs1486915	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17079785	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17290490	0.83[EUR][1000 genomes]
rs2030596	0.87[EUR][1000 genomes]
rs2047559	0.87[EUR][1000 genomes]
rs2049301	0.85[EUR][1000 genomes]
rs2101398	0.88[EUR][1000 genomes]
rs2133601	0.86[EUR][1000 genomes]
rs2140335	0.80[EUR][1000 genomes]
rs319693	0.83[EUR][1000 genomes]
rs34351471	0.92[EUR][1000 genomes]
rs34569417	0.90[EUR][1000 genomes]
rs34777284	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34906469	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35148469	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35167544	0.84[AMR][1000 genomes]
rs35582375	0.87[EUR][1000 genomes]
rs35664069	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35698005	0.93[EUR][1000 genomes]
rs3772399	0.88[EUR][1000 genomes]
rs3888	0.90[EUR][1000 genomes]
rs3915654	0.88[EUR][1000 genomes]
rs4410463	0.87[EUR][1000 genomes]
rs4858851	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858853	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858857	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4858860	0.90[EUR][1000 genomes]
rs4858863	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55823596	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56376646	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61181421	0.93[EUR][1000 genomes]
rs61675361	0.89[AMR][1000 genomes]
rs62262129	0.86[EUR][1000 genomes]
rs62263575	0.88[EUR][1000 genomes]
rs6442079	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442081	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6442082	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6442083	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6442085	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6442086	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6768699	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6772301	0.85[EUR][1000 genomes]
rs6773467	0.85[EUR][1000 genomes]
rs6773732	0.85[EUR][1000 genomes]
rs6776963	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6777632	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6782998	0.86[EUR][1000 genomes]
rs6785669	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6786001	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6792350	0.94[EUR][1000 genomes]
rs6792497	0.87[EUR][1000 genomes]
rs6792737	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6806860	0.94[EUR][1000 genomes]
rs72906488	0.93[EUR][1000 genomes]
rs73085151	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7429162	0.85[EUR][1000 genomes]
rs7612219	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7618758	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7629850	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637372	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7637950	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7638103	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7645846	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7646982	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7649393	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs869508	0.87[AMR][1000 genomes]
rs883662	0.91[AMR][1000 genomes]
rs9757517	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9850154	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv876758	chr3:47681881-47842234	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
3	nsv876759	chr3:47725315-47830741	Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	nsv834679	chr3:47749475-47924006	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs62263561	NME6	cis	Esophagus Muscularis	GTEx
rs62263561	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs62263561	MRPS18AP1	cis	Nerve Tibial	GTEx
rs62263561	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs62263561	ZNF589	cis	Nerve Tibial	GTEx
rs62263561	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs62263561	MRPS18AP1	cis	lung	GTEx
rs62263561	MRPS18AP1	cis	Artery Tibial	GTEx
rs62263561	ZNF589	cis	Whole Blood	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47701600-47800400	Strong transcription	Dnd41	blood
2	chr3:47701600-47819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:47727600-47819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47769600-47812400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:47769800-47817800	Weak transcription	Pancreas	Pancrea
6	chr3:47772800-47821000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:47774200-47799000	Weak transcription	NHEK	skin
8	chr3:47774200-47820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:47777000-47817600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:47777200-47794000	Weak transcription	Psoas Muscle	Psoas
11	chr3:47777200-47801400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:47777200-47805200	Weak transcription	Esophagus	oesophagus
13	chr3:47777200-47812400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:47777200-47813600	Weak transcription	A549	lung
15	chr3:47777200-47819000	Weak transcription	Fetal Brain Male	brain
16	chr3:47777200-47819800	Weak transcription	Small Intestine	intestine
17	chr3:47777400-47799600	Weak transcription	Spleen	Spleen
18	chr3:47777400-47802000	Weak transcription	Aorta	Aorta
19	chr3:47777400-47805400	Weak transcription	Gastric	stomach
20	chr3:47777400-47805600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:47777400-47812600	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:47777400-47819800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:47777400-47821000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:47777400-47821000	Weak transcription	Brain Substantia Nigra	brain
25	chr3:47777400-47821800	Weak transcription	Right Ventricle	heart
26	chr3:47777600-47798200	Weak transcription	Brain Anterior Caudate	brain
27	chr3:47777600-47812800	Weak transcription	NHDF-Ad	bronchial
28	chr3:47777600-47820600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:47777600-47820800	Weak transcription	NHLF	lung
30	chr3:47777800-47802000	Weak transcription	Fetal Kidney	kidney
31	chr3:47778800-47798200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:47778800-47805400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr3:47778800-47814200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:47781200-47802600	Weak transcription	Ovary	ovary
35	chr3:47784000-47816000	Strong transcription	Fetal Stomach	stomach
36	chr3:47784400-47811800	Weak transcription	Left Ventricle	heart
37	chr3:47784600-47793800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:47784800-47799400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:47784800-47820800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:47785200-47805400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:47785600-47798200	Weak transcription	Hela-S3	cervix
42	chr3:47785600-47803600	Weak transcription	Fetal Heart	heart
43	chr3:47786200-47793600	Strong transcription	Fetal Intestine Small	intestine
44	chr3:47786400-47805400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:47786600-47794200	Weak transcription	Liver	Liver
46	chr3:47786600-47805000	Weak transcription	HMEC	breast
47	chr3:47786600-47814200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:47786800-47793800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:47786800-47793800	Weak transcription	NH-A	brain
50	chr3:47786800-47798000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links