Variant report

Variant	rs9878058
Chromosome Location	chr3:105388605-105388606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:105388584..105391376-chr3:105413040..105414567,2	MCF-7	breast:
2	chr3:105388597..105390954-chr3:105393490..105396667,3	MCF-7	breast:
3	chr3:105384518..105386462-chr3:105388169..105391773,3	MCF-7	breast:

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1042852	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10446294	0.81[AMR][1000 genomes]
rs11706886	0.80[AMR][1000 genomes]
rs11713094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11915926	0.82[AMR][1000 genomes]
rs11929289	0.83[AMR][1000 genomes]
rs12493181	0.83[AMR][1000 genomes]
rs12493560	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12695122	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12695123	0.83[AMR][1000 genomes]
rs13059405	0.83[AMR][1000 genomes]
rs13061160	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13064310	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13065142	0.83[AMR][1000 genomes]
rs13070917	0.86[ASN][1000 genomes]
rs13083716	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13084260	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13093260	0.83[AMR][1000 genomes]
rs13315174	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13317635	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1443105	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1443106	0.87[AMR][1000 genomes]
rs1443108	0.87[AMR][1000 genomes]
rs1530420	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1545304	0.94[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17202230	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17202348	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1867189	0.86[AMR][1000 genomes]
rs1867190	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2083758	0.83[AMR][1000 genomes]
rs2083761	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2120585	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2244737	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2284993	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2301029	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2301030	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2301032	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2301037	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301040	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301041	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301043	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301050	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2301051	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2305035	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2305036	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2305037	0.86[AMR][1000 genomes]
rs2399054	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2399055	0.83[AMR][1000 genomes]
rs28532512	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs34520191	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34896116	0.83[AMR][1000 genomes]
rs35748894	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35834008	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs3732554	0.89[ASN][1000 genomes]
rs3772513	0.80[AMR][1000 genomes]
rs3772515	0.83[AMR][1000 genomes]
rs3772521	0.80[AMR][1000 genomes]
rs3772526	0.86[AMR][1000 genomes]
rs3772527	0.86[AMR][1000 genomes]
rs3772531	0.86[AMR][1000 genomes]
rs3772536	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772537	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821488	0.87[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4321559	0.83[AMR][1000 genomes]
rs4627779	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6437611	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437614	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6773661	0.83[AMR][1000 genomes]
rs6796643	0.82[AMR][1000 genomes]
rs726444	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7615317	0.84[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7619647	0.82[AMR][1000 genomes]
rs7624530	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7646445	0.87[AMR][1000 genomes]
rs7649520	0.80[AMR][1000 genomes]
rs7652702	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs894937	0.86[AMR][1000 genomes]
rs9288815	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9657914	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9657915	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9816486	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9821956	0.80[CEU][hapmap]
rs9840891	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9860539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9870097	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9872897	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9873552	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9876767	0.83[AMR][1000 genomes]
rs9877805	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9880861	0.83[AMR][1000 genomes]
rs9883858	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs999046	0.87[AMR][1000 genomes];0.82[ASN][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
rs9878058	CBLB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105368800-105393400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:105373000-105419600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:105373400-105401600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:105373600-105419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:105373800-105406200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:105374200-105392600	Weak transcription	Psoas Muscle	Psoas
7	chr3:105374800-105392800	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:105375000-105395600	Weak transcription	Brain Anterior Caudate	brain
9	chr3:105375200-105395400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:105375200-105395600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:105375800-105389200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:105375800-105399000	Weak transcription	Dnd41	blood
13	chr3:105375800-105405000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:105375800-105419600	Weak transcription	Colonic Mucosa	Colon
15	chr3:105375800-105464600	Weak transcription	Small Intestine	intestine
16	chr3:105376000-105395600	Weak transcription	Esophagus	oesophagus
17	chr3:105376000-105438200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:105376200-105397200	Weak transcription	NHLF	lung
19	chr3:105376400-105395600	Weak transcription	Fetal Brain Male	brain
20	chr3:105376800-105395400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:105376800-105440000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr3:105377200-105399200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:105378000-105392600	Weak transcription	Ovary	ovary
24	chr3:105378000-105395600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:105378000-105420800	Weak transcription	HUVEC	blood vessel
26	chr3:105378000-105455400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:105378600-105438600	Weak transcription	Spleen	Spleen
28	chr3:105378800-105393400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:105379000-105392400	Weak transcription	Fetal Brain Female	brain
30	chr3:105379000-105437400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:105379200-105440400	Weak transcription	Thymus	Thymus
32	chr3:105379600-105391800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:105380600-105411800	Weak transcription	Brain Substantia Nigra	brain
34	chr3:105382200-105404800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:105382400-105392400	Weak transcription	Fetal Kidney	kidney
36	chr3:105382400-105395600	Weak transcription	Pancreas	Pancrea
37	chr3:105382400-105397200	Weak transcription	Lung	lung
38	chr3:105382400-105405000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:105382800-105404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:105383800-105398600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:105384200-105400000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:105384600-105404600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:105385000-105389200	Strong transcription	Primary B cells from cord blood	blood
44	chr3:105385000-105390400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:105385000-105404600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:105385200-105398000	Strong transcription	HSMM	muscle
47	chr3:105385200-105404400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:105385400-105405200	Strong transcription	Osteobl	bone
49	chr3:105385400-105411000	Weak transcription	HMEC	breast
50	chr3:105385600-105388800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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