Variant report

Variant	rs16832733
Chromosome Location	chr1:161228843-161228844
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	chr1:161227745..161230399-chr1:161282979..161284618,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143252	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11265571	0.88[ASN][1000 genomes]
rs11584174	0.83[CHB][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[ASN][1000 genomes]
rs12029543	0.87[ASN][1000 genomes]
rs12030706	0.88[ASN][1000 genomes]
rs12032041	0.88[ASN][1000 genomes]
rs12041050	0.88[ASN][1000 genomes]
rs12116949	1.00[LWK][hapmap]
rs12565792	0.87[ASN][1000 genomes]
rs12721035	1.00[LWK][hapmap];1.00[MEX][hapmap]
rs28470413	0.87[ASN][1000 genomes]
rs28559311	0.87[ASN][1000 genomes]
rs4077629	1.00[YRI][hapmap]
rs4609448	0.87[ASN][1000 genomes]
rs4656998	0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs4656999	0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs55802895	0.87[ASN][1000 genomes]
rs56835010	0.88[ASN][1000 genomes]
rs6413453	1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap]
rs6686001	0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs72714938	0.87[ASN][1000 genomes]
rs7532292	0.88[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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16832733	NDUFS2	cis	parietal	SCAN
rs16832733	PAQR6	cis	cerebellum	SCAN
rs16832733	NDUFS2	cis	cerebellum	SCAN
rs16832733	PPOX	cis	cerebellum	SCAN
rs16832733	ITLN2	cis	cerebellum	SCAN
rs16832733	NOS1AP,C1orf226	cis	temporal cortex	BrainEAC
rs16832733	YY1AP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161228000-161229000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:161228000-161229200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:161228000-161229200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:161228000-161229200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:161228200-161229000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr1:161228200-161229000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:161228200-161229000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:161228200-161229000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
9	chr1:161228200-161229000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr1:161228200-161229000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
11	chr1:161228200-161229000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
12	chr1:161228200-161229000	Active TSS	Brain Anterior Caudate	brain
13	chr1:161228200-161229000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
14	chr1:161228200-161229000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
15	chr1:161228200-161229000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
16	chr1:161228200-161229000	Active TSS	Right Atrium	heart
17	chr1:161228200-161229000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
18	chr1:161228200-161229000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
19	chr1:161228200-161229200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:161228200-161229200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
21	chr1:161228200-161229200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr1:161228200-161229200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:161228200-161229200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
24	chr1:161228200-161229200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:161228200-161229200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:161228200-161229200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:161228200-161229200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:161228200-161229200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:161228200-161229200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
30	chr1:161228200-161229200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
31	chr1:161228200-161229200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
32	chr1:161228200-161229200	Bivalent/Poised TSS	A549	lung
33	chr1:161228200-161229400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:161228200-161229400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr1:161228200-161229400	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr1:161228200-161229400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:161228200-161229400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
38	chr1:161228200-161229400	Active TSS	Brain Substantia Nigra	brain
39	chr1:161228200-161229600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr1:161228400-161229000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:161228400-161229000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:161228400-161229000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:161228400-161229000	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr1:161228400-161229000	Bivalent/Poised TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:161228400-161229000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
46	chr1:161228400-161229000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
47	chr1:161228400-161229000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
48	chr1:161228400-161229000	Active TSS	Esophagus	oesophagus
49	chr1:161228400-161229000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
50	chr1:161228400-161229000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet

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