Variant report

Variant	rs4858853
Chromosome Location	chr3:47802095-47802096
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47798148..47800331-chr3:47801413..47803600,2	K562	blood:
2	chr3:47801338..47803180-chr3:47822974..47824547,2	K562	blood:

Variant related genes	Relation type
ENSG00000173473	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs11130147	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130148	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130150	0.86[EUR][1000 genomes]
rs11707707	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11708849	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11710199	0.83[EUR][1000 genomes]
rs11712152	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11712464	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11714942	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11927129	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11929303	0.87[AMR][1000 genomes]
rs12495204	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12635438	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12636198	0.87[AMR][1000 genomes]
rs13063042	0.84[EUR][1000 genomes]
rs13064183	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13069142	0.86[AMR][1000 genomes]
rs13070035	0.91[EUR][1000 genomes]
rs13077230	0.86[EUR][1000 genomes]
rs13079407	0.83[EUR][1000 genomes]
rs13085978	0.89[AMR][1000 genomes]
rs13086149	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13091913	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13094264	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13098128	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13319205	0.84[EUR][1000 genomes]
rs1486915	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17079785	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17290490	0.82[EUR][1000 genomes]
rs2030596	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2047559	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2049301	0.84[EUR][1000 genomes]
rs2101398	0.89[EUR][1000 genomes]
rs2133601	0.85[EUR][1000 genomes]
rs319693	0.82[EUR][1000 genomes]
rs34351471	0.91[EUR][1000 genomes]
rs34569417	0.91[EUR][1000 genomes]
rs34777284	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34906469	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35148469	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35167544	0.84[AMR][1000 genomes]
rs35582375	0.86[EUR][1000 genomes]
rs35664069	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35698005	0.95[EUR][1000 genomes]
rs3772399	0.89[EUR][1000 genomes]
rs3888	0.92[EUR][1000 genomes]
rs3915654	0.89[EUR][1000 genomes]
rs4410463	0.86[EUR][1000 genomes]
rs4858851	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4858857	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858860	0.92[EUR][1000 genomes]
rs4858863	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55823596	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56376646	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61181421	0.95[EUR][1000 genomes]
rs61675361	0.89[AMR][1000 genomes]
rs62262129	0.85[EUR][1000 genomes]
rs62263561	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62263575	0.89[EUR][1000 genomes]
rs6442079	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6442081	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442082	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6442083	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6442085	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442086	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6768699	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6772301	0.84[EUR][1000 genomes]
rs6773467	0.84[EUR][1000 genomes]
rs6773732	0.84[EUR][1000 genomes]
rs6776963	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6777632	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6782998	0.85[EUR][1000 genomes]
rs6785669	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6786001	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6792350	0.95[EUR][1000 genomes]
rs6792497	0.86[EUR][1000 genomes]
rs6792737	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6806860	0.93[EUR][1000 genomes]
rs72906488	0.95[EUR][1000 genomes]
rs73085151	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7429162	0.84[EUR][1000 genomes]
rs7612219	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7618758	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7629850	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637372	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7637950	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7638103	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7645846	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7646982	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7649393	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs869508	0.87[AMR][1000 genomes]
rs883662	0.91[AMR][1000 genomes]
rs9757517	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9850154	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv590233	chr3:47798700-47829277	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4858853	ZNF589	cis	Nerve Tibial	GTEx
rs4858853	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs4858853	MRPS18AP1	cis	Artery Tibial	GTEx
rs4858853	MRPS18AP1	cis	Nerve Tibial	GTEx
rs4858853	NME6	cis	Esophagus Muscularis	GTEx
rs4858853	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs4858853	MRPS18AP1	cis	lung	GTEx
rs4858853	ZNF589	cis	Whole Blood	GTEx
rs4858853	DHX30	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47701600-47819800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:47727600-47819400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47769600-47812400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:47769800-47817800	Weak transcription	Pancreas	Pancrea
5	chr3:47772800-47821000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:47774200-47820600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:47777000-47817600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr3:47777200-47805200	Weak transcription	Esophagus	oesophagus
9	chr3:47777200-47812400	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:47777200-47813600	Weak transcription	A549	lung
11	chr3:47777200-47819000	Weak transcription	Fetal Brain Male	brain
12	chr3:47777200-47819800	Weak transcription	Small Intestine	intestine
13	chr3:47777400-47805400	Weak transcription	Gastric	stomach
14	chr3:47777400-47805600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:47777400-47812600	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:47777400-47819800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:47777400-47821000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:47777400-47821000	Weak transcription	Brain Substantia Nigra	brain
19	chr3:47777400-47821800	Weak transcription	Right Ventricle	heart
20	chr3:47777600-47812800	Weak transcription	NHDF-Ad	bronchial
21	chr3:47777600-47820600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:47777600-47820800	Weak transcription	NHLF	lung
23	chr3:47778800-47805400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:47778800-47814200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:47781200-47802600	Weak transcription	Ovary	ovary
26	chr3:47784000-47816000	Strong transcription	Fetal Stomach	stomach
27	chr3:47784400-47811800	Weak transcription	Left Ventricle	heart
28	chr3:47784800-47820800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:47785200-47805400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:47785600-47803600	Weak transcription	Fetal Heart	heart
31	chr3:47786400-47805400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:47786600-47805000	Weak transcription	HMEC	breast
33	chr3:47786600-47814200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:47787200-47808200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:47787200-47811000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:47787400-47805400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:47787400-47808000	Weak transcription	Adipose Nuclei	Adipose
38	chr3:47787400-47811800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:47787400-47812600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:47787400-47820800	Weak transcription	Brain Angular Gyrus	brain
41	chr3:47787600-47805600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:47787800-47805400	Weak transcription	HSMM	muscle
43	chr3:47788000-47813600	Weak transcription	HUVEC	blood vessel
44	chr3:47788200-47805200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:47788800-47805200	Weak transcription	Lung	lung
46	chr3:47793000-47802800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:47793000-47818000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:47793400-47803200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:47793800-47814800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:47794000-47803600	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links