Variant report

Variant	rs3772515
Chromosome Location	chr3:105486255-105486256
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1042852	0.92[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10446294	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11706886	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11713094	0.83[AMR][1000 genomes]
rs11915926	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11929289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12486371	1.00[ASW][hapmap]
rs12493181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12493560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12695122	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12695123	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13059405	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13061160	0.88[AMR][1000 genomes]
rs13064310	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13065142	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13083716	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13084260	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13093260	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13315174	0.83[AMR][1000 genomes]
rs13317635	0.92[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs1443105	0.91[CEU][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1443106	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1443108	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1530420	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1545304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17202230	0.83[AMR][1000 genomes]
rs17202348	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1838046	0.84[EUR][1000 genomes]
rs1867189	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1867190	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2083758	0.95[CEU][hapmap];0.94[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]
rs2083761	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2120585	0.87[CEU][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2244737	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2284993	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2301029	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2301030	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2301032	0.88[AMR][1000 genomes]
rs2301037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2301040	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2301041	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2301043	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2301050	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2301051	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2305035	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2305036	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2305037	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2399054	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2399055	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28532512	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34520191	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34896116	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35748894	0.83[AMR][1000 genomes]
rs35834008	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3772513	0.96[CEU][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3772521	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772526	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772527	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772531	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772536	0.89[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap]
rs3772537	0.90[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]
rs3821488	0.94[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes]
rs4321559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4627779	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6437611	0.81[AMR][1000 genomes]
rs6437614	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6773661	0.95[CEU][hapmap];0.94[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];0.99[ASN][1000 genomes]
rs6796643	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs726444	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7615317	0.86[AMR][1000 genomes]
rs7619647	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7624530	0.92[ASW][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs7639888	0.92[ASW][hapmap]
rs7641825	0.85[ASW][hapmap]
rs7646445	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7649520	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7652702	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs894937	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9288815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9657914	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9657915	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9816486	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9840891	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs9860539	0.83[AMR][1000 genomes]
rs9870097	0.82[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9872897	0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9873552	0.80[AMR][1000 genomes]
rs9876110	0.92[ASW][hapmap]
rs9876767	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9877805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs9878058	0.83[AMR][1000 genomes]
rs9880861	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9883858	0.80[AMR][1000 genomes]
rs999046	0.91[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3772515	CBLB	Cis_1M	lymphoblastoid	RTeQTL
rs3772515	CD47	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
2	chr3:105472200-105499000	Weak transcription	NHDF-Ad	bronchial
3	chr3:105472400-105504400	Weak transcription	HUVEC	blood vessel
4	chr3:105476000-105486600	Weak transcription	Psoas Muscle	Psoas
5	chr3:105477800-105486800	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:105478200-105495400	Weak transcription	HSMMtube	muscle
7	chr3:105478600-105486600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:105478600-105509400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:105478600-105511200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:105478800-105489200	Weak transcription	Right Atrium	heart
11	chr3:105478800-105496200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:105481200-105500800	Weak transcription	Small Intestine	intestine
13	chr3:105481400-105491600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:105481400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:105481600-105486600	Weak transcription	Adipose Nuclei	Adipose
16	chr3:105481600-105486600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:105481600-105498000	Weak transcription	NH-A	brain
18	chr3:105481800-105507400	Weak transcription	HSMM	muscle
19	chr3:105482000-105486600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:105482000-105486600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:105482000-105486600	Weak transcription	Liver	Liver
22	chr3:105482000-105486600	Weak transcription	Esophagus	oesophagus
23	chr3:105482000-105492400	Weak transcription	HepG2	liver
24	chr3:105482000-105496200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:105482000-105496200	Weak transcription	Lung	lung
26	chr3:105482000-105503800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:105482000-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:105482000-105509600	Weak transcription	Ovary	ovary
29	chr3:105482000-105510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:105482000-105511200	Weak transcription	Aorta	Aorta
31	chr3:105482200-105494600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr3:105482400-105486400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:105482400-105486600	Weak transcription	Left Ventricle	heart
34	chr3:105482400-105486600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:105482400-105489400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:105482400-105489800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:105482400-105493600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:105482400-105494400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:105482400-105500000	Weak transcription	Fetal Stomach	stomach
40	chr3:105482600-105486400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:105482600-105486600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:105482600-105487600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:105482600-105487600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr3:105482800-105486600	Weak transcription	Fetal Lung	lung
45	chr3:105482800-105487800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr3:105482800-105489000	Weak transcription	Fetal Intestine Small	intestine
47	chr3:105482800-105489400	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
49	chr3:105483000-105486600	Weak transcription	Fetal Kidney	kidney
50	chr3:105483000-105491400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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