Variant report

Variant	rs16830450
Chromosome Location	chr2:152779752-152779753
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152778363..152780861-chr2:152784387..152786073,2	MCF-7	breast:
2	chr2:152774858..152777174-chr2:152778629..152781508,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10930837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930853	0.92[ASN][1000 genomes]
rs12463883	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12469117	0.83[EUR][1000 genomes]
rs1356732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1474172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1519710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16830434	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16830435	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16830539	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs3754532	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3820703	0.83[EUR][1000 genomes]
rs4496331	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs4563220	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs66900149	0.83[EUR][1000 genomes]
rs6730903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67572576	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7562260	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7571876	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7580901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7581344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7597915	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs867544	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs883157	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap]
rs883170	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs952339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16830450	XBP1	trans	brain	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152767800-152780400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:152775400-152779800	Weak transcription	Left Ventricle	heart
3	chr2:152775800-152784000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:152776000-152783800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:152776200-152779800	Weak transcription	Lung	lung
6	chr2:152776200-152779800	Weak transcription	Spleen	Spleen
7	chr2:152776400-152781600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:152778200-152780200	Enhancers	Placenta	Placenta
9	chr2:152778200-152780600	Enhancers	HUVEC	blood vessel
10	chr2:152778600-152779800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:152778600-152780200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:152778600-152780200	Enhancers	Esophagus	oesophagus
13	chr2:152778800-152780200	Enhancers	Psoas Muscle	Psoas
14	chr2:152778800-152780400	Enhancers	Adipose Nuclei	Adipose
15	chr2:152779000-152779800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:152779000-152780000	Enhancers	Right Atrium	heart
17	chr2:152779200-152780000	Enhancers	Primary B cells from cord blood	blood
18	chr2:152779200-152780200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:152779200-152780400	Enhancers	NHEK	skin
20	chr2:152779400-152779800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:152779400-152779800	Flanking Active TSS	Fetal Heart	heart
22	chr2:152779400-152780200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr2:152779400-152780200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:152779400-152780200	Enhancers	Colon Smooth Muscle	Colon
25	chr2:152779400-152780200	Enhancers	Fetal Muscle Leg	muscle
26	chr2:152779400-152780200	Enhancers	Right Ventricle	heart
27	chr2:152779400-152780200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr2:152779400-152780400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr2:152779400-152780400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:152779400-152780400	Enhancers	Brain Anterior Caudate	brain
31	chr2:152779400-152780400	Enhancers	Brain Hippocampus Middle	brain
32	chr2:152779600-152779800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:152779600-152780000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr2:152779600-152780200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:152779600-152780400	Enhancers	HepG2	liver
36	chr2:152779600-152780400	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links