Variant report

Variant	rs12233086
Chromosome Location	chr2:99978048-99978049
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99952304..99954680-chr2:99976875..99979040,2	K562	blood:
2	chr2:99971535..99975686-chr2:99976476..99979996,5	K562	blood:
3	chr2:99977104..99978712-chr2:99988658..99990955,2	MCF-7	breast:
4	chr2:99977638..99980361-chr2:99981242..99982894,2	K562	blood:
5	chr2:99965212..99967140-chr2:99975946..99978198,2	K562	blood:
6	chr2:99952346..99954433-chr2:99975150..99979293,3	K562	blood:

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction
ENSG00000158417	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1011633	0.89[JPT][hapmap]
rs10207981	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs1053544	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs11123775	0.89[JPT][hapmap]
rs11123785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11884686	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs11892441	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs11899745	0.89[JPT][hapmap]
rs12053519	0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12053566	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12233126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12464785	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1451245	0.82[ASW][hapmap];0.91[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap]
rs1584647	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs1584648	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs17022433	0.89[JPT][hapmap]
rs17022564	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs17022629	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2200578	0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2242036	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2290255	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2290257	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2290261	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2309617	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs28369925	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28382892	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28382949	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3087395	0.81[MEX][hapmap]
rs3749087	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3791212	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs3791213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792135	0.82[ASW][hapmap];0.91[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.84[YRI][hapmap]
rs3792136	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3792137	0.89[JPT][hapmap]
rs3792138	0.81[MEX][hapmap]
rs3792142	0.88[JPT][hapmap]
rs4143760	0.89[JPT][hapmap]
rs4851206	0.89[JPT][hapmap]
rs57043099	0.80[AMR][1000 genomes]
rs57169028	0.80[EUR][1000 genomes]
rs57550691	0.81[EUR][1000 genomes]
rs58766196	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59360884	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60572342	0.83[AMR][1000 genomes]
rs6715321	0.89[JPT][hapmap]
rs6722617	0.86[CHD][hapmap];0.84[JPT][hapmap]
rs6727483	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6728175	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6728936	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs717454	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs72954262	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72954283	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72954284	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72954287	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72956308	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72956312	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72956317	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72956346	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72956387	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72958366	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72958380	0.81[AMR][1000 genomes]
rs7563462	0.89[JPT][hapmap]
rs7585019	0.89[JPT][hapmap]
rs7593274	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs7597141	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs769105	0.89[JPT][hapmap]
rs896248	0.87[JPT][hapmap]
rs896249	0.89[JPT][hapmap]
rs9941566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv874699	chr2:99898998-100010044	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12233086	COX5B	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99955000-99979200	Weak transcription	Fetal Stomach	stomach
2	chr2:99955000-99979800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:99955200-99979600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:99955200-99982600	Weak transcription	Fetal Brain Male	brain
5	chr2:99955400-99979600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:99955400-99979600	Weak transcription	NH-A	brain
7	chr2:99955600-99978200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
9	chr2:99956400-99979600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:99956400-99979600	Weak transcription	HUVEC	blood vessel
11	chr2:99957400-99978200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:99957600-99989400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:99957800-99978200	Weak transcription	Hela-S3	cervix
14	chr2:99958000-99978800	Weak transcription	Fetal Intestine Small	intestine
15	chr2:99958200-99979600	Weak transcription	A549	lung
16	chr2:99959800-99980000	Weak transcription	Lung	lung
17	chr2:99961200-99979400	Weak transcription	Ovary	ovary
18	chr2:99962400-99979800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:99962400-99979800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:99965600-99979800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:99969400-99981600	Weak transcription	Fetal Brain Female	brain
22	chr2:99970800-99979200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr2:99970800-99979600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:99970800-99979600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:99970800-99979800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:99970800-99979800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:99971000-99978200	Weak transcription	Osteobl	bone
28	chr2:99971000-99979600	Weak transcription	HMEC	breast
29	chr2:99973200-99979800	Weak transcription	Aorta	Aorta
30	chr2:99973400-99979600	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:99973400-99979600	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:99973400-99979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr2:99973400-99982600	Weak transcription	Psoas Muscle	Psoas
34	chr2:99973800-99979800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:99973800-99982200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:99974200-99979400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:99974200-99979800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:99974400-99978200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:99974400-99979800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:99974400-99979800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:99974400-99979800	Weak transcription	HSMMtube	muscle
42	chr2:99974400-99981600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:99974600-99978200	Weak transcription	Brain Germinal Matrix	brain
44	chr2:99974800-99984000	Weak transcription	Pancreas	Pancrea
45	chr2:99975000-99979800	Weak transcription	Gastric	stomach
46	chr2:99975000-99981800	Weak transcription	Thymus	Thymus
47	chr2:99975200-99978200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:99975200-99980800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:99975200-99980800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:99975400-99979800	Weak transcription	Fetal Lung	lung

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