Variant report

Variant	rs239261
Chromosome Location	chr11:64993357-64993358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64988866..64990383-chr11:64992045..64994203,2	K562	blood:
2	chr11:64901949..64903595-chr11:64993216..64995733,2	MCF-7	breast:
3	chr11:64992394..64994754-chr11:64999110..65001538,2	MCF-7	breast:
4	chr11:64991684..64993403-chr11:65306861..65309115,2	K562	blood:
5	chr11:64986935..64989872-chr11:64992647..64995488,2	MCF-7	breast:
6	chr11:64980421..64987264-chr11:64991140..64994999,6	K562	blood:
7	chr11:64980421..64983038-chr11:64992029..64994539,2	K562	blood:
8	chr11:64983043..64986391-chr11:64991756..64994999,4	K562	blood:
9	chr11:64992972..64993724-chr11:65082707..65083305,4	K562	blood:
10	chr11:64957988..64959551-chr11:64991502..64993463,2	K562	blood:
11	chr11:64490664..64492722-chr11:64991494..64993936,2	MCF-7	breast:
12	chr11:64992795..64993731-chr11:65017504..65018445,4	MCF-7	breast:
13	chr11:64992503..64993651-chr11:65017553..65018631,3	K562	blood:
14	chr11:64899551..64901557-chr11:64993119..64995072,2	K562	blood:
15	chr11:64982257..64984604-chr11:64993334..64996229,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197847	Chromatin interaction
ENSG00000168056	Chromatin interaction
ENSG00000162298	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10750761	0.91[ASN][1000 genomes]
rs1195733	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1633466	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1783486	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs1858783	0.80[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs1877450	0.91[ASN][1000 genomes]
rs239257	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2904966	0.88[CEU][hapmap];0.91[GIH][hapmap]
rs2904967	0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap]
rs2904979	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2904980	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2904981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2904982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes]
rs2904983	0.93[ASN][1000 genomes]
rs2904984	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2957111	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3015997	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3015999	0.80[ASN][1000 genomes]
rs3016001	0.89[ASN][1000 genomes]
rs3016002	0.88[ASN][1000 genomes]
rs482842	0.80[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];0.81[YRI][hapmap]
rs487989	0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap]
rs503277	1.00[JPT][hapmap]
rs506280	1.00[JPT][hapmap]
rs507005	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs509303	0.94[CHD][hapmap]
rs526502	0.89[CHD][hapmap];0.82[GIH][hapmap]
rs541829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs554122	0.80[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs560097	0.80[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap]
rs571128	0.81[ASN][1000 genomes]
rs592050	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs611910	0.80[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs612392	0.84[ASW][hapmap];0.88[CEU][hapmap];0.88[MEX][hapmap];0.86[YRI][hapmap]
rs620427	0.82[ASW][hapmap];0.88[CEU][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap]
rs625427	0.93[ASN][1000 genomes]
rs626555	1.00[JPT][hapmap]
rs626802	0.80[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs630055	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs655433	1.00[JPT][hapmap]
rs6591180	0.84[YRI][hapmap]
rs667341	0.80[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs668735	0.80[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs673147	0.80[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap]
rs676114	0.94[CHD][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.86[YRI][hapmap]
rs676573	1.00[JPT][hapmap]
rs689288	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs7111907	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7116674	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap]
rs8638	1.00[JPT][hapmap]

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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897713	chr11:64915042-65000719	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	nsv832190	chr11:64978144-65127613	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS 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	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs239261	POLA2	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64977400-64998400	Weak transcription	Small Intestine	intestine
2	chr11:64981800-64993400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:64992200-64993800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr11:64992200-64994000	Enhancers	Stomach Mucosa	stomach
5	chr11:64992400-64993400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr11:64992400-64993400	Enhancers	A549	lung
7	chr11:64992400-64993600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr11:64992400-64993600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr11:64992400-64993600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:64992600-64993400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr11:64992600-64993600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:64992600-64993600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:64992600-64993600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr11:64992600-64993600	Enhancers	Lung	lung
15	chr11:64992600-64993600	Flanking Active TSS	K562	blood
16	chr11:64992600-64993800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr11:64992600-64993800	Flanking Active TSS	Osteobl	bone
18	chr11:64992600-64994000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr11:64992600-64994000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:64992800-64993400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:64992800-64993400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr11:64992800-64993600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:64992800-64993600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:64992800-64993600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:64992800-64993600	Enhancers	Fetal Heart	heart
26	chr11:64992800-64993600	Flanking Active TSS	Placenta	Placenta
27	chr11:64992800-64993600	Enhancers	HSMMtube	muscle
28	chr11:64992800-64993600	Flanking Active TSS	HUVEC	blood vessel
29	chr11:64992800-64993800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr11:64992800-64993800	Active TSS	Primary T cells from cord blood	blood
31	chr11:64992800-64993800	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr11:64992800-64993800	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr11:64992800-64993800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
34	chr11:64992800-64993800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr11:64992800-64993800	Flanking Active TSS	HMEC	breast
36	chr11:64992800-64993800	Flanking Active TSS	NHEK	skin
37	chr11:64992800-64994000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr11:64992800-64994000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:64992800-64994000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:64992800-64994000	Active TSS	Rectal Smooth Muscle	rectum
41	chr11:64992800-64994000	Flanking Active TSS	GM12878-XiMat	blood
42	chr11:64992800-64994000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr11:64993000-64993400	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr11:64993000-64993400	Active TSS	Brain Cingulate Gyrus	brain
45	chr11:64993000-64993400	Active TSS	Colon Smooth Muscle	Colon
46	chr11:64993000-64993400	Active TSS	Duodenum Mucosa	Duodenum
47	chr11:64993000-64993400	Active TSS	Gastric	stomach
48	chr11:64993000-64993400	Active TSS	Left Ventricle	heart
49	chr11:64993000-64993400	Active TSS	Placenta Amnion	Placenta Amnion
50	chr11:64993000-64993400	Transcr. at gene 5' and 3'	Right Atrium	heart

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