Variant report

Variant	rs16851630
Chromosome Location	chr3:105533713-105533714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105529832..105533992-chr3:105585756..105590627,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114423	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10460808	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10511246	0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1075739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11921710	0.88[ASN][1000 genomes]
rs12633654	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12635232	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12637560	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637809	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12639271	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1561922	0.82[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844736	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs16851523	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16851539	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16851563	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16851570	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16851587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867192	0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs1947000	0.82[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992521	0.82[EUR][1000 genomes]
rs2089091	0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2197208	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2197209	0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2301036	0.82[EUR][1000 genomes]
rs3772540	0.82[CEU][hapmap]
rs57520912	0.88[ASN][1000 genomes]
rs58340800	0.88[ASN][1000 genomes]
rs59534462	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59611997	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60295307	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60619938	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6437620	0.89[ASN][1000 genomes]
rs6437621	0.89[ASN][1000 genomes]
rs73854891	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73854894	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73857222	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7624400	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7629357	0.86[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7648842	0.89[ASN][1000 genomes]
rs9631436	0.88[ASN][1000 genomes]
rs9789988	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9826886	0.89[ASN][1000 genomes]
rs9846534	0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs9874600	0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16851630	CBLB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
2	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
4	chr3:105512200-105534200	Weak transcription	Left Ventricle	heart
5	chr3:105515400-105539000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:105519200-105541600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:105521200-105536000	Weak transcription	Right Ventricle	heart
8	chr3:105521200-105546800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:105521400-105541200	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:105521400-105542000	Weak transcription	Fetal Stomach	stomach
11	chr3:105522400-105533800	Weak transcription	Brain Germinal Matrix	brain
12	chr3:105522400-105541200	Weak transcription	Primary T cells from cord blood	blood
13	chr3:105524600-105541600	Weak transcription	Right Atrium	heart
14	chr3:105525600-105540200	Weak transcription	NHLF	lung
15	chr3:105526200-105534000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr3:105526200-105541600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:105526200-105542400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:105527600-105537800	Weak transcription	Primary B cells from cord blood	blood
19	chr3:105528400-105541600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:105528400-105542000	Weak transcription	Pancreas	Pancrea
21	chr3:105528400-105543200	Weak transcription	Gastric	stomach
22	chr3:105528400-105553600	Weak transcription	Fetal Kidney	kidney
23	chr3:105528600-105542600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:105528800-105536600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:105528800-105539000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:105528800-105539000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:105528800-105540000	Weak transcription	Fetal Heart	heart
28	chr3:105528800-105540200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:105528800-105541600	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:105529000-105540000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:105529000-105541600	Weak transcription	Fetal Lung	lung
32	chr3:105529000-105541800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:105529000-105542200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:105529000-105546600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:105529600-105533800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:105530400-105536400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:105530400-105537800	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:105530400-105540400	Weak transcription	Adipose Nuclei	Adipose
39	chr3:105530400-105541600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:105530400-105542000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:105530600-105540400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:105530600-105541800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:105530800-105541800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:105531000-105535600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:105531400-105536200	Weak transcription	NH-A	brain
46	chr3:105531400-105539200	Weak transcription	Liver	Liver
47	chr3:105531400-105540200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:105531400-105540200	Weak transcription	HSMMtube	muscle
49	chr3:105531400-105546600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:105531600-105535600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links