Variant report

Variant	rs9833231
Chromosome Location	chr3:88079581-88079582
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	chr3:88079170..88082380-chr3:88083202..88085793,3	MCF-7	breast:
2	chr3:88079258..88082127-chr3:88106343..88109218,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229729	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11128023	1.00[EUR][1000 genomes]
rs12632860	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1367615	1.00[EUR][1000 genomes]
rs1431154	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431155	1.00[ASN][1000 genomes]
rs1431156	1.00[ASN][1000 genomes]
rs1469570	1.00[ASN][1000 genomes]
rs1594453	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1594455	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604700	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1835544	1.00[ASN][1000 genomes]
rs1897238	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033390	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2344183	1.00[ASN][1000 genomes]
rs2344184	1.00[ASN][1000 genomes]
rs2567037	1.00[EUR][1000 genomes]
rs2735557	1.00[EUR][1000 genomes]
rs2880793	1.00[ASN][1000 genomes]
rs4241549	1.00[EUR][1000 genomes]
rs4241550	1.00[EUR][1000 genomes]
rs4287925	1.00[EUR][1000 genomes]
rs4404474	1.00[EUR][1000 genomes]
rs4425287	1.00[EUR][1000 genomes]
rs4431134	1.00[ASN][1000 genomes]
rs4443201	1.00[EUR][1000 genomes]
rs4513473	1.00[EUR][1000 genomes]
rs4515075	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858927	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858933	1.00[EUR][1000 genomes]
rs4858970	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858989	1.00[EUR][1000 genomes]
rs6551270	1.00[EUR][1000 genomes]
rs6767497	1.00[ASN][1000 genomes]
rs7615309	1.00[EUR][1000 genomes]
rs7621357	1.00[EUR][1000 genomes]
rs7625641	1.00[EUR][1000 genomes]
rs7633486	1.00[EUR][1000 genomes]
rs7636845	1.00[EUR][1000 genomes]
rs7650749	0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650912	1.00[EUR][1000 genomes]
rs7650915	1.00[EUR][1000 genomes]
rs930154	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930155	1.00[ASN][1000 genomes]
rs9310062	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310063	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9310064	1.00[ASN][1000 genomes]
rs9310069	1.00[EUR][1000 genomes]
rs9310073	1.00[EUR][1000 genomes]
rs9812903	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850550	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854250	1.00[ASN][1000 genomes]
rs9860113	1.00[EUR][1000 genomes]
rs9864564	1.00[EUR][1000 genomes]
rs9867614	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv536635	chr3:88049304-88088520	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88073600-88080600	Weak transcription	Thymus	Thymus
2	chr3:88078200-88080800	Weak transcription	Left Ventricle	heart
3	chr3:88079200-88079600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:88079200-88079600	Active TSS	Liver	Liver
5	chr3:88079200-88079600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:88079200-88079600	Active TSS	Monocytes-CD14+_RO01746	blood
7	chr3:88079200-88079800	Active TSS	Primary T helper naive cells from peripheral blood	blood
8	chr3:88079200-88079800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:88079200-88079800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr3:88079200-88079800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:88079200-88079800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:88079200-88079800	Active TSS	Adipose Nuclei	Adipose
13	chr3:88079200-88079800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr3:88079200-88079800	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr3:88079200-88080000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:88079200-88080400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:88079200-88080600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:88079200-88081400	Active TSS	GM12878-XiMat	blood
19	chr3:88079400-88079600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:88079400-88079600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:88079400-88079600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:88079400-88079600	Active TSS	HUVEC	blood vessel
23	chr3:88079400-88079800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:88079400-88079800	Active TSS	Primary T cells fromperipheralblood	blood
25	chr3:88079400-88079800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr3:88079400-88079800	Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr3:88079400-88079800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr3:88079400-88079800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:88079400-88079800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr3:88079400-88079800	Active TSS	Colon Smooth Muscle	Colon
31	chr3:88079400-88079800	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr3:88079400-88079800	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr3:88079400-88079800	Active TSS	A549	lung
34	chr3:88079400-88079800	Flanking Active TSS	Dnd41	blood
35	chr3:88079400-88079800	Active TSS	NHLF	lung
36	chr3:88079400-88079800	Active TSS	Osteobl	bone
37	chr3:88079400-88080400	Active TSS	Primary T cells from cord blood	blood
38	chr3:88079400-88080400	Active TSS	Primary hematopoietic stem cells	blood
39	chr3:88079400-88081800	Active TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links