Variant report

Variant	rs1546733
Chromosome Location	chr3:105409321-105409322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11708360	0.82[AMR][1000 genomes]
rs13061514	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1372982	0.84[CEU][hapmap]
rs1522287	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1550711	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1561919	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1584028	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16851440	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1867191	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2034157	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2120105	1.00[CHB][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2293148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2301044	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301046	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35903551	0.86[AMR][1000 genomes]
rs3772539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4476538	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4894940	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4894944	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6767808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6787175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6800344	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726443	1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes]
rs7612189	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7640740	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7645026	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs9832882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9873655	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9876007	0.89[AMR][1000 genomes];0.93[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	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
3	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
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1546733	CBLB	Cis_1M	lymphoblastoid	RTeQTL
rs1546733	CD47	cis	cerebellum	SCAN
rs1546733	CBLB	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105373000-105419600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105373600-105419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:105375800-105419600	Weak transcription	Colonic Mucosa	Colon
4	chr3:105375800-105464600	Weak transcription	Small Intestine	intestine
5	chr3:105376000-105438200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:105376800-105440000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:105378000-105420800	Weak transcription	HUVEC	blood vessel
8	chr3:105378000-105455400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:105378600-105438600	Weak transcription	Spleen	Spleen
10	chr3:105379000-105437400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:105379200-105440400	Weak transcription	Thymus	Thymus
12	chr3:105380600-105411800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:105385400-105411000	Weak transcription	HMEC	breast
14	chr3:105387200-105420800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:105388400-105421000	Weak transcription	Gastric	stomach
16	chr3:105388600-105419800	Weak transcription	Brain Germinal Matrix	brain
17	chr3:105389200-105467200	Weak transcription	Stomach Mucosa	stomach
18	chr3:105393600-105420800	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:105394200-105438800	Weak transcription	NHEK	skin
20	chr3:105396000-105411800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:105396000-105420200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:105396000-105420800	Weak transcription	Brain Angular Gyrus	brain
23	chr3:105396000-105432600	Weak transcription	Pancreas	Pancrea
24	chr3:105396000-105437200	Weak transcription	Psoas Muscle	Psoas
25	chr3:105396000-105437400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:105396000-105438200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:105396000-105438400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:105396200-105430400	Weak transcription	Fetal Brain Male	brain
29	chr3:105397600-105410600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:105397600-105411200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:105397800-105410000	Weak transcription	Fetal Heart	heart
32	chr3:105397800-105419600	Weak transcription	Fetal Thymus	thymus
33	chr3:105399600-105419600	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:105399600-105420000	Weak transcription	Right Ventricle	heart
35	chr3:105400000-105437200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:105400200-105411000	Weak transcription	Fetal Kidney	kidney
37	chr3:105400200-105420600	Weak transcription	Brain Anterior Caudate	brain
38	chr3:105400400-105410400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:105400400-105419600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:105400600-105409800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:105400600-105410400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:105400600-105410600	Weak transcription	Dnd41	blood
43	chr3:105400600-105410800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:105400600-105411600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:105400600-105411600	Weak transcription	Fetal Brain Female	brain
46	chr3:105400600-105411800	Weak transcription	Ovary	ovary
47	chr3:105400600-105419600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:105400600-105419600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr3:105400600-105419600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:105400600-105420800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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