Variant report

Variant	rs9873552
Chromosome Location	chr3:105382315-105382316
allele	A/C
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:82)

rs_ID	r²[population]
rs1042852	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10446294	0.82[ASN][1000 genomes]
rs11713094	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11929289	0.80[AMR][1000 genomes]
rs12493181	0.80[AMR][1000 genomes]
rs12493560	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12695122	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12695123	0.80[AMR][1000 genomes]
rs13059405	0.80[AMR][1000 genomes]
rs13061160	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13064310	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13065142	0.80[AMR][1000 genomes]
rs13083716	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13084260	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13093260	0.80[AMR][1000 genomes]
rs13315174	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13317635	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1443105	0.84[AMR][1000 genomes]
rs1443106	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1443108	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1530420	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1545304	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17202230	0.84[AMR][1000 genomes]
rs17202348	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1867189	0.83[AMR][1000 genomes]
rs1867190	0.89[AMR][1000 genomes]
rs2083758	0.80[AMR][1000 genomes]
rs2083761	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2120585	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2244737	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2284993	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2301029	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2301030	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2301032	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2301037	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301040	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301041	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301043	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301050	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2301051	0.85[AMR][1000 genomes]
rs2305035	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2305036	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2305037	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2399054	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2399055	0.80[AMR][1000 genomes]
rs28532512	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34520191	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34896116	0.80[AMR][1000 genomes]
rs35748894	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35834008	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3772515	0.80[AMR][1000 genomes]
rs3772526	0.83[AMR][1000 genomes]
rs3772527	0.83[AMR][1000 genomes]
rs3772531	0.83[AMR][1000 genomes]
rs3772536	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3772537	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3821488	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4321559	0.80[AMR][1000 genomes]
rs4627779	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6437611	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6437614	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6773661	0.80[AMR][1000 genomes]
rs726444	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7615317	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7624530	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7646445	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7652702	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs894937	0.83[AMR][1000 genomes]
rs9288815	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9657914	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9657915	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9816486	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9840891	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9860539	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9870097	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9872897	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9876767	0.80[AMR][1000 genomes]
rs9877805	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9878058	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9880861	0.80[AMR][1000 genomes]
rs9883858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999046	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv877306	chr3:105372196-105495841	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv877307	chr3:105373836-105465189	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv591242	chr3:105373836-105470134	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv877308	chr3:105373836-105495841	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9873552	CBLB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105368800-105388400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:105368800-105393400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:105372200-105387400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:105372400-105388000	Weak transcription	Stomach Mucosa	stomach
5	chr3:105373000-105387800	Weak transcription	Gastric	stomach
6	chr3:105373000-105419600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:105373400-105401600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:105373600-105419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:105373800-105406200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:105374200-105388400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:105374200-105392600	Weak transcription	Psoas Muscle	Psoas
12	chr3:105374400-105388000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:105374800-105392800	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:105375000-105388000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:105375000-105395600	Weak transcription	Brain Anterior Caudate	brain
16	chr3:105375200-105395400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:105375200-105395600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:105375600-105382800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:105375600-105383600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr3:105375800-105382800	Strong transcription	Primary T cells from cord blood	blood
21	chr3:105375800-105384200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr3:105375800-105389200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:105375800-105399000	Weak transcription	Dnd41	blood
24	chr3:105375800-105405000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:105375800-105419600	Weak transcription	Colonic Mucosa	Colon
26	chr3:105375800-105464600	Weak transcription	Small Intestine	intestine
27	chr3:105376000-105382800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:105376000-105384200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:105376000-105395600	Weak transcription	Esophagus	oesophagus
30	chr3:105376000-105438200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:105376200-105383800	Strong transcription	Primary B cells from cord blood	blood
32	chr3:105376200-105383800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:105376200-105397200	Weak transcription	NHLF	lung
34	chr3:105376400-105395600	Weak transcription	Fetal Brain Male	brain
35	chr3:105376600-105384000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:105376800-105382600	Strong transcription	Fetal Intestine Large	intestine
37	chr3:105376800-105395400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:105376800-105440000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr3:105377200-105382600	Strong transcription	Fetal Lung	lung
40	chr3:105377200-105385000	Strong transcription	Left Ventricle	heart
41	chr3:105377200-105399200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:105378000-105387600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:105378000-105387800	Weak transcription	HepG2	liver
44	chr3:105378000-105388000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:105378000-105392600	Weak transcription	Ovary	ovary
46	chr3:105378000-105395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:105378000-105420800	Weak transcription	HUVEC	blood vessel
48	chr3:105378000-105455400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:105378200-105388000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:105378400-105385600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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