Variant report

Variant	rs1550711
Chromosome Location	chr3:105465189-105465190
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10804442	0.94[ASW][hapmap];0.83[YRI][hapmap]
rs11708360	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060223	1.00[ASW][hapmap]
rs13061514	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1372982	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1443102	0.88[YRI][hapmap]
rs1522287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1546733	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	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584028	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851440	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1867191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992522	0.82[YRI][hapmap]
rs2010718	0.82[ASN][1000 genomes]
rs2034157	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2120105	0.83[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2289746	0.80[TSI][hapmap]
rs2293148	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2301044	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2301045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2301046	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2399056	0.83[YRI][hapmap]
rs35903551	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3772539	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4476538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894940	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4894944	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4894950	0.83[YRI][hapmap]
rs6437612	0.85[EUR][1000 genomes]
rs6437624	1.00[ASW][hapmap]
rs6767808	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6777124	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6787175	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6795961	1.00[ASW][hapmap];0.83[YRI][hapmap]
rs6800344	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs726443	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7612189	0.81[ASN][1000 genomes]
rs7640740	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644634	0.84[EUR][1000 genomes]
rs7645026	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7646159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7651784	1.00[ASW][hapmap]
rs769315	1.00[ASW][hapmap];0.83[YRI][hapmap]
rs9832882	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9841500	1.00[ASW][hapmap]
rs9873655	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9876007	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv591243	chr3:105438320-105470134	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
9	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
10	nsv591245	chr3:105438806-105469882	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
11	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
12	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1550711	CBLB	cis	multi-tissue	Pritchard
rs1550711	CD47	cis	cerebellum	SCAN
rs1550711	CBLB	cis	cerebellum	SCAN
rs1550711	CBLB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105389200-105467200	Weak transcription	Stomach Mucosa	stomach
2	chr3:105421200-105465400	Weak transcription	Colonic Mucosa	Colon
3	chr3:105433600-105465600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:105438800-105465400	Weak transcription	Fetal Heart	heart
5	chr3:105439000-105465400	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:105439000-105465800	Weak transcription	NHLF	lung
7	chr3:105439000-105466200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:105439000-105466600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:105439000-105471200	Weak transcription	Fetal Thymus	thymus
10	chr3:105439000-105471400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr3:105439000-105471400	Weak transcription	HMEC	breast
12	chr3:105439000-105471600	Weak transcription	Fetal Brain Male	brain
13	chr3:105439000-105475800	Weak transcription	Esophagus	oesophagus
14	chr3:105439000-105477400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:105439000-105477400	Weak transcription	Lung	lung
16	chr3:105439000-105477400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:105439200-105465200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:105439200-105465400	Weak transcription	Ovary	ovary
19	chr3:105439200-105465400	Weak transcription	Psoas Muscle	Psoas
20	chr3:105439200-105465600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:105439200-105465600	Weak transcription	Right Ventricle	heart
22	chr3:105439200-105465600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:105439200-105477200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:105439600-105465200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:105445800-105465600	Weak transcription	Gastric	stomach
26	chr3:105446600-105477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:105448600-105465400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:105449000-105465400	Weak transcription	Aorta	Aorta
29	chr3:105450400-105465400	Strong transcription	Osteobl	bone
30	chr3:105451200-105465200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:105452400-105465400	Weak transcription	Left Ventricle	heart
32	chr3:105452400-105477400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:105452800-105477400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:105453600-105465400	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:105455000-105465200	Strong transcription	Placenta	Placenta
36	chr3:105458000-105475600	Weak transcription	Pancreas	Pancrea
37	chr3:105459600-105465200	Weak transcription	HepG2	liver
38	chr3:105460200-105471600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:105460800-105466000	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr3:105461800-105465400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr3:105462000-105470200	Weak transcription	Dnd41	blood
42	chr3:105463000-105465200	Weak transcription	Brain Substantia Nigra	brain
43	chr3:105463000-105465400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:105463200-105465600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:105463200-105471400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr3:105463400-105465200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:105463400-105465400	Weak transcription	HSMM	muscle
48	chr3:105463400-105470800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:105463800-105465200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:105464000-105465400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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