Variant report

Variant	rs2399055
Chromosome Location	chr3:105470758-105470759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1042852	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10446294	0.82[AMR][1000 genomes]
rs10490830	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs11706886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11713094	0.83[AMR][1000 genomes]
rs11915926	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11929289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12493560	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12695122	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12695123	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13059405	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13061160	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13062734	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs13064310	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13065142	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13070917	0.93[CHB][hapmap]
rs13073784	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs13082334	0.93[CHB][hapmap];0.89[ASN][1000 genomes]
rs13083716	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13084260	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13093260	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13315174	0.83[AMR][1000 genomes]
rs13317635	0.83[AMR][1000 genomes]
rs1443105	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1443106	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1443108	0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1530420	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1545304	0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17202230	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17202348	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1867189	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1867190	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2083758	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2083761	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2120585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2244737	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2284993	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2301029	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2301030	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2301032	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2301037	0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2301040	0.81[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2301041	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2301043	0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2301050	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2301051	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2305035	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2305036	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2305037	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2399054	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs28532512	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34520191	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34896116	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35748894	0.83[AMR][1000 genomes]
rs35834008	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3732554	0.86[CHB][hapmap]
rs3772513	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772515	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772521	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3772526	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772527	0.81[CHB][hapmap];0.90[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3772531	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3772536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3772537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs3821488	0.83[AMR][1000 genomes]
rs4321559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4627779	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6437611	0.81[AMR][1000 genomes]
rs6437614	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6773661	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6796643	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726444	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7615317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7619647	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7624530	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs7646445	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7649520	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7652702	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs894937	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9288815	0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9657914	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9657915	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9816486	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9840891	0.80[AMR][1000 genomes]
rs9860539	0.83[AMR][1000 genomes]
rs9870097	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9872897	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9873552	0.80[AMR][1000 genomes]
rs9876767	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9877805	0.83[AMR][1000 genomes]
rs9878058	0.83[AMR][1000 genomes]
rs9880861	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9883858	0.80[AMR][1000 genomes]
rs999046	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv877310	chr3:105409321-105495841	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv591244	chr3:105438320-105495841	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv591246	chr3:105439522-105504129	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv877311	chr3:105449986-105493286	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2399055	CBLB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105439000-105471200	Weak transcription	Fetal Thymus	thymus
2	chr3:105439000-105471400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:105439000-105471400	Weak transcription	HMEC	breast
4	chr3:105439000-105471600	Weak transcription	Fetal Brain Male	brain
5	chr3:105439000-105475800	Weak transcription	Esophagus	oesophagus
6	chr3:105439000-105477400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:105439000-105477400	Weak transcription	Lung	lung
8	chr3:105439000-105477400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:105439200-105477200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:105446600-105477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:105452400-105477400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:105452800-105477400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:105458000-105475600	Weak transcription	Pancreas	Pancrea
14	chr3:105460200-105471600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:105463200-105471400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:105463400-105470800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:105464200-105471000	Enhancers	Primary T cells from cord blood	blood
18	chr3:105464200-105477400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:105464200-105478200	Weak transcription	Right Atrium	heart
20	chr3:105464400-105477400	Weak transcription	Fetal Lung	lung
21	chr3:105464600-105471200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:105464600-105477400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:105464800-105477400	Weak transcription	Liver	Liver
24	chr3:105464800-105477400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:105464800-105482600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:105465000-105471200	Weak transcription	HSMMtube	muscle
27	chr3:105465000-105472000	Weak transcription	HUVEC	blood vessel
28	chr3:105465200-105471200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:105465400-105471200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:105465600-105471200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:105465600-105471400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr3:105465600-105478200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:105465800-105471200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:105465800-105471200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr3:105465800-105471400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:105465800-105471400	Weak transcription	HSMM	muscle
37	chr3:105465800-105471600	Weak transcription	Gastric	stomach
38	chr3:105465800-105477200	Weak transcription	Fetal Stomach	stomach
39	chr3:105465800-105477400	Weak transcription	Fetal Intestine Large	intestine
40	chr3:105465800-105477400	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:105465800-105477400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:105465800-105483400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:105466000-105470800	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr3:105466000-105471600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:105466000-105477200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:105466000-105477200	Weak transcription	Right Ventricle	heart
47	chr3:105466000-105477400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:105466000-105481200	Weak transcription	Fetal Kidney	kidney
49	chr3:105466200-105471000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:105466200-105477400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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