Variant report

Variant	rs4683723
Chromosome Location	chr3:142754236-142754237
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10413	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1043898	0.94[EUR][1000 genomes]
rs10451867	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10513184	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1053950	0.95[EUR][1000 genomes]
rs10790	0.88[EUR][1000 genomes]
rs10935475	0.87[EUR][1000 genomes]
rs10935479	0.94[EUR][1000 genomes]
rs11709036	0.82[EUR][1000 genomes]
rs11915462	0.89[EUR][1000 genomes]
rs11922201	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12485790	0.82[EUR][1000 genomes]
rs12490776	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492904	0.88[EUR][1000 genomes]
rs12695770	0.82[EUR][1000 genomes]
rs13075955	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13088422	0.86[EUR][1000 genomes]
rs13094293	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13099995	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1349262	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13715	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1375814	0.90[EUR][1000 genomes]
rs1449868	0.91[EUR][1000 genomes]
rs1449869	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1530753	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1532588	0.90[EUR][1000 genomes]
rs1545597	0.83[EUR][1000 genomes]
rs17557029	0.88[EUR][1000 genomes]
rs1814565	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1827159	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1839406	0.91[EUR][1000 genomes]
rs1868569	0.93[EUR][1000 genomes]
rs1868570	0.93[EUR][1000 genomes]
rs1965343	0.90[EUR][1000 genomes]
rs2045306	0.95[EUR][1000 genomes]
rs2124541	0.90[EUR][1000 genomes]
rs2124542	0.87[EUR][1000 genomes]
rs2124543	0.87[EUR][1000 genomes]
rs2137586	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2175739	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290549	0.85[EUR][1000 genomes]
rs2353408	0.92[EUR][1000 genomes]
rs2353409	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2353411	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821645	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3856697	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3902877	0.88[EUR][1000 genomes]
rs4030582	0.90[EUR][1000 genomes]
rs4683444	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683721	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683722	0.91[EUR][1000 genomes]
rs4683724	0.91[EUR][1000 genomes]
rs56382522	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440129	0.90[EUR][1000 genomes]
rs6440131	0.94[EUR][1000 genomes]
rs6440132	0.92[EUR][1000 genomes]
rs6440133	0.87[EUR][1000 genomes]
rs6440134	0.95[EUR][1000 genomes]
rs6770102	0.87[EUR][1000 genomes]
rs6778454	0.87[EUR][1000 genomes]
rs6781080	0.91[EUR][1000 genomes]
rs6781887	0.90[EUR][1000 genomes]
rs6783145	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6796771	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6802376	0.81[EUR][1000 genomes]
rs6805417	0.94[EUR][1000 genomes]
rs6806551	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6808689	0.91[EUR][1000 genomes]
rs7611721	0.91[EUR][1000 genomes]
rs7623532	0.94[EUR][1000 genomes]
rs7644475	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7648143	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7649225	0.88[EUR][1000 genomes]
rs7652745	0.89[EUR][1000 genomes]
rs766360	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs936194	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs936196	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs936197	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs937498	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9814656	0.94[EUR][1000 genomes]
rs9816317	0.95[EUR][1000 genomes]
rs9820175	0.80[EUR][1000 genomes]
rs9835348	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9847059	0.93[EUR][1000 genomes]
rs9851353	0.93[EUR][1000 genomes]
rs9862433	0.92[EUR][1000 genomes]
rs9877128	0.94[EUR][1000 genomes]
rs9877135	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4683723	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142721800-142761800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:142727400-142764400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:142728600-142769000	Weak transcription	Pancreas	Pancrea
4	chr3:142729200-142758600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:142729200-142765000	Strong transcription	Dnd41	blood
6	chr3:142729200-142785200	Weak transcription	Aorta	Aorta
7	chr3:142729400-142764800	Strong transcription	K562	blood
8	chr3:142729800-142764800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:142729800-142765000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:142730200-142765000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:142730200-142765000	Strong transcription	Fetal Thymus	thymus
12	chr3:142730800-142758800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:142732800-142759000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:142732800-142765000	Strong transcription	HSMM	muscle
15	chr3:142733000-142755000	Weak transcription	Stomach Mucosa	stomach
16	chr3:142733200-142764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:142734000-142758800	Strong transcription	Liver	Liver
18	chr3:142734400-142759000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:142734400-142785200	Weak transcription	Esophagus	oesophagus
20	chr3:142734600-142758800	Strong transcription	GM12878-XiMat	blood
21	chr3:142734800-142756400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:142735000-142758800	Strong transcription	Placenta	Placenta
23	chr3:142735600-142759400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr3:142735600-142759400	Strong transcription	NHDF-Ad	bronchial
25	chr3:142735800-142758600	Strong transcription	Primary hematopoietic stem cells	blood
26	chr3:142739000-142754800	Strong transcription	Fetal Intestine Large	intestine
27	chr3:142740000-142769200	Weak transcription	Gastric	stomach
28	chr3:142740200-142763200	Weak transcription	Lung	lung
29	chr3:142742400-142764800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr3:142742600-142764200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:142743000-142755400	Weak transcription	Brain Germinal Matrix	brain
32	chr3:142743600-142763200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:142743600-142764400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:142744600-142759400	Strong transcription	Primary T cells from cord blood	blood
35	chr3:142745800-142754400	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr3:142745800-142756400	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:142745800-142757600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:142745800-142758800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr3:142746000-142758400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr3:142746000-142759400	Strong transcription	Primary B cells from cord blood	blood
41	chr3:142747000-142761800	Weak transcription	Fetal Brain Male	brain
42	chr3:142747800-142756400	Strong transcription	Colon Smooth Muscle	Colon
43	chr3:142748200-142755400	Weak transcription	Brain Substantia Nigra	brain
44	chr3:142748200-142755400	Weak transcription	NHEK	skin
45	chr3:142748800-142754800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:142748800-142755400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:142748800-142755400	Weak transcription	NHLF	lung
48	chr3:142748800-142762000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:142749000-142755400	Weak transcription	Fetal Heart	heart
50	chr3:142749000-142755400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links