Variant report

Variant	rs4340582
Chromosome Location	chr2:133405068-133405069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:133403144..133405262-chr2:133426855..133428605,2	MCF-7	breast:
2	chr2:133397006..133400489-chr2:133401960..133405775,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR39-5	chr2:133403922-133405535	ucscGeneNc_uc002ttr_2

Variant related genes	Relation type
ENSG00000150551	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10179167	0.93[ASN][1000 genomes]
rs10179785	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10189715	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1131671	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13028563	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1430630	0.92[ASN][1000 genomes]
rs1430631	0.94[ASN][1000 genomes]
rs1430632	0.92[ASN][1000 genomes]
rs17396523	0.94[ASN][1000 genomes]
rs17396537	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17396607	0.95[ASN][1000 genomes]
rs1897166	0.88[ASN][1000 genomes]
rs2082177	0.81[ASN][1000 genomes]
rs2082179	0.87[ASN][1000 genomes]
rs2082181	0.84[ASN][1000 genomes]
rs2163342	0.92[ASN][1000 genomes]
rs2244888	0.87[ASN][1000 genomes]
rs2248193	0.87[ASN][1000 genomes]
rs2288653	0.92[ASN][1000 genomes]
rs2315599	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2320153	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2435612	0.92[ASN][1000 genomes]
rs2566528	0.87[ASN][1000 genomes]
rs2566529	0.85[ASN][1000 genomes]
rs2566530	0.83[ASN][1000 genomes]
rs2566535	0.84[ASN][1000 genomes]
rs2566536	0.88[ASN][1000 genomes]
rs2566537	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2566538	0.92[ASN][1000 genomes]
rs2709520	0.87[ASN][1000 genomes]
rs2709521	0.87[ASN][1000 genomes]
rs2709523	0.91[ASN][1000 genomes]
rs2709524	0.92[ASN][1000 genomes]
rs2709525	0.89[ASN][1000 genomes]
rs2709526	0.94[ASN][1000 genomes]
rs2709527	0.92[ASN][1000 genomes]
rs2709528	0.91[ASN][1000 genomes]
rs2709532	0.86[ASN][1000 genomes]
rs2709533	0.84[ASN][1000 genomes]
rs2709545	0.82[ASN][1000 genomes]
rs2709546	0.81[ASN][1000 genomes]
rs2709548	0.87[ASN][1000 genomes]
rs2709549	0.86[ASN][1000 genomes]
rs3738842	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4547577	0.84[ASN][1000 genomes]
rs4547578	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4954351	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4954352	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs713535	0.94[ASN][1000 genomes]
rs721470	0.86[ASN][1000 genomes]
rs744821	0.82[ASN][1000 genomes]
rs7558213	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558730	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7567602	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7603894	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7603926	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7608591	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9973717	0.85[EUR][1000 genomes];0.95[ASN][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	nsv1011421	chr2:132895241-133682185	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv875137	chr2:133167263-133714142	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv583155	chr2:133253386-133415170	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133390200-133412600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:133390400-133413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:133390400-133423800	Weak transcription	A549	lung
4	chr2:133390800-133405400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr2:133398600-133406000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:133399000-133408800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:133399800-133410800	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:133400200-133405200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:133402000-133405800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:133402200-133406600	Weak transcription	HUVEC	blood vessel
11	chr2:133403000-133409200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:133403000-133419600	Weak transcription	Fetal Kidney	kidney
13	chr2:133403200-133409400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:133403400-133405200	Weak transcription	Pancreas	Pancrea
15	chr2:133403600-133405400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:133403800-133409200	Weak transcription	Fetal Brain Male	brain
17	chr2:133404000-133410000	Weak transcription	Fetal Stomach	stomach
18	chr2:133404000-133411400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:133404000-133413800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:133404000-133426000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:133404200-133408000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:133404200-133412600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:133404400-133413600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:133404600-133406400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:133404600-133406400	Weak transcription	Fetal Intestine Large	intestine
26	chr2:133404600-133408800	Weak transcription	Fetal Intestine Small	intestine
27	chr2:133404600-133409200	Weak transcription	NH-A	brain
28	chr2:133404600-133409400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:133404600-133410200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:133404600-133413600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:133404800-133409000	Weak transcription	Fetal Brain Female	brain
32	chr2:133404800-133409800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:133405000-133409400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links