Variant report

Variant	rs1042852
Chromosome Location	chr3:105377515-105377516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10446294	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11706886	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11713094	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11915926	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11929289	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12486371	0.91[ASW][hapmap]
rs12493181	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12493560	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs12695122	0.80[AMR][1000 genomes]
rs12695123	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13059405	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13064310	0.83[AMR][1000 genomes]
rs13065142	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13083716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084260	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093260	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13315174	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13317635	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1443105	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1443106	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1443108	0.92[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1530420	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1545304	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17202230	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17202348	0.80[AMR][1000 genomes]
rs1867189	0.92[ASW][hapmap];0.87[CEU][hapmap];0.96[GIH][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1867190	0.80[AMR][1000 genomes]
rs2083758	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2083761	0.83[AMR][1000 genomes]
rs2120585	0.95[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2244737	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2284993	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301029	0.80[AMR][1000 genomes]
rs2301030	0.80[AMR][1000 genomes]
rs2301037	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2301040	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2301041	0.83[AMR][1000 genomes]
rs2301043	0.92[ASW][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs2301050	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301051	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2305035	0.92[ASW][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes]
rs2305036	0.92[ASW][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs2305037	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2399054	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs2399055	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28532512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34520191	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34896116	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35748894	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35834008	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772513	0.87[CEU][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3772515	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]
rs3772521	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3772526	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3772527	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3772531	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3772536	0.81[GIH][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs3772537	0.83[ASW][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3821488	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4321559	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4627779	0.82[AMR][1000 genomes]
rs6437611	0.86[AMR][1000 genomes]
rs6437614	0.80[AMR][1000 genomes]
rs6773661	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6796643	0.88[AMR][1000 genomes]
rs726444	0.83[AMR][1000 genomes]
rs7615317	0.81[AMR][1000 genomes]
rs7619647	0.92[ASW][hapmap];0.83[CEU][hapmap];0.96[GIH][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes]
rs7624530	1.00[ASW][hapmap];0.81[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7639888	0.84[ASW][hapmap]
rs7646445	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7649520	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7652702	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs894937	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9288815	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs9657914	0.95[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9657915	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9816486	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840891	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9860539	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9870097	0.95[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9872897	0.80[AMR][1000 genomes]
rs9873552	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9876110	0.84[ASW][hapmap]
rs9876767	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9877805	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9878058	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9880861	0.92[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.80[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]
rs9883858	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs999046	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.82[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1042852	CBLB	Cis_1M	lymphoblastoid	RTeQTL
rs1042852	CD47	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105367400-105377600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:105368800-105377600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:105368800-105388400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:105368800-105393400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:105371400-105382200	Weak transcription	Lung	lung
6	chr3:105372000-105381800	Weak transcription	Pancreas	Pancrea
7	chr3:105372200-105380800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:105372200-105387400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr3:105372400-105388000	Weak transcription	Stomach Mucosa	stomach
10	chr3:105373000-105377600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:105373000-105381800	Weak transcription	Right Ventricle	heart
12	chr3:105373000-105387800	Weak transcription	Gastric	stomach
13	chr3:105373000-105419600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:105373400-105401600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:105373600-105419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:105373800-105406200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:105374200-105388400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:105374200-105392600	Weak transcription	Psoas Muscle	Psoas
19	chr3:105374400-105388000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:105374800-105381000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:105374800-105392800	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:105375000-105388000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:105375000-105395600	Weak transcription	Brain Anterior Caudate	brain
24	chr3:105375200-105395400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:105375200-105395600	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:105375400-105377600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:105375400-105377600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:105375600-105380600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:105375600-105381000	Weak transcription	Aorta	Aorta
30	chr3:105375600-105382800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:105375600-105383600	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:105375800-105377600	Weak transcription	Spleen	Spleen
33	chr3:105375800-105379000	Strong transcription	Fetal Muscle Leg	muscle
34	chr3:105375800-105381200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:105375800-105382800	Strong transcription	Primary T cells from cord blood	blood
36	chr3:105375800-105384200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr3:105375800-105389200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:105375800-105399000	Weak transcription	Dnd41	blood
39	chr3:105375800-105405000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:105375800-105419600	Weak transcription	Colonic Mucosa	Colon
41	chr3:105375800-105464600	Weak transcription	Small Intestine	intestine
42	chr3:105376000-105377600	Weak transcription	Fetal Thymus	thymus
43	chr3:105376000-105377600	Weak transcription	Thymus	Thymus
44	chr3:105376000-105379800	Strong transcription	Adipose Nuclei	Adipose
45	chr3:105376000-105380000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr3:105376000-105381400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:105376000-105382800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:105376000-105384200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:105376000-105395600	Weak transcription	Esophagus	oesophagus
50	chr3:105376000-105438200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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