Variant report

Variant	rs10732253
Chromosome Location	chr11:67006400-67006401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr11:67006381-67007723	K562	blood:	n/a	n/a
2	CHD1	chr11:67006078-67009359	IMR90	lung:	n/a	n/a
3	MXI1	chr11:67005794-67009327	SK-N-SH	brain:	n/a	chr11:67008781-67008796
4	EP300	chr11:67006342-67006970	SK-N-SH_RA	brain:	n/a	chr11:67006416-67006429
5	MAZ	chr11:67006251-67009143	IMR90	lung:	n/a	chr11:67007354-67007364 chr11:67008724-67008733 chr11:67008724-67008733 chr11:67008724-67008733 chr11:67008787-67008796
6	EP300	chr11:67006376-67006704	SK-N-SH_RA	brain:	n/a	chr11:67006416-67006429

No.	Distal block	Cell Line	Cell type
1	chr11:67006044..67008912-chr11:67118920..67122236,4	K562	blood:
2	chr11:66885002..66889173-chr11:67005085..67009324,11	K562	blood:
3	chr11:66884916..66890908-chr11:67005112..67010354,8	MCF-7	breast:
4	chr11:67005795..67007805-chr16:3072226..3074419,2	MCF-7	breast:
5	chr11:66883623..66889678-chr11:67005085..67009894,16	K562	blood:
6	chr11:66820676..66825699-chr11:67004753..67010986,10	MCF-7	breast:

Variant related genes	Relation type
KDM2A	TF binding region
ENSG00000175482	Chromatin interaction
ENSG00000103145	Chromatin interaction
ENSG00000131652	Chromatin interaction
ENSG00000173156	Chromatin interaction
ENSG00000173120	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10400320	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10750796	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896171	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11227699	1.00[GIH][hapmap]
rs11227771	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11227780	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1253784	1.00[ASW][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1894111	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2228522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2255990	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs3741189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815364	1.00[CHB][hapmap]
rs3825022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4271388	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4344498	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57327069	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57478329	0.81[EUR][1000 genomes]
rs57724865	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58224869	1.00[EUR][1000 genomes]
rs59057433	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59817822	0.94[EUR][1000 genomes]
rs61180657	0.82[ASN][1000 genomes]
rs61663253	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs645387	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];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655168	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs682509	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];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7937611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7941655	0.89[JPT][hapmap]

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	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv532287	chr11:66784014-67023899	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10732253	RPS6KB2	cis	lymphoblastoid	seeQTL
rs10732253	RPS6KB2	cis	multi-tissue	Pritchard

Chromatin state (count:186 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66965200-67006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:66981800-67006400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:66995800-67006400	Weak transcription	Fetal Brain Male	brain
4	chr11:66996400-67006400	Weak transcription	Aorta	Aorta
5	chr11:66996400-67006400	Weak transcription	Ovary	ovary
6	chr11:66996600-67006400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:66996600-67006400	Weak transcription	Colonic Mucosa	Colon
8	chr11:66996600-67006400	Weak transcription	Psoas Muscle	Psoas
9	chr11:66998200-67006400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:66999400-67006400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr11:66999400-67006400	Weak transcription	Pancreas	Pancrea
12	chr11:66999600-67006400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:66999600-67006400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:66999600-67006400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:66999600-67006400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:66999600-67006400	Weak transcription	Right Ventricle	heart
17	chr11:66999600-67006400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:66999600-67006400	Weak transcription	A549	lung
19	chr11:67000000-67006400	Weak transcription	Fetal Brain Female	brain
20	chr11:67000200-67007600	Weak transcription	Small Intestine	intestine
21	chr11:67001400-67006400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr11:67001400-67006400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:67001600-67006400	Weak transcription	Placenta	Placenta
24	chr11:67002000-67006400	Weak transcription	NH-A	brain
25	chr11:67002400-67006400	Weak transcription	Esophagus	oesophagus
26	chr11:67002400-67006400	Weak transcription	Gastric	stomach
27	chr11:67002400-67006400	Weak transcription	Lung	lung
28	chr11:67002400-67006400	Weak transcription	Spleen	Spleen
29	chr11:67002800-67006600	Weak transcription	Brain Germinal Matrix	brain
30	chr11:67003200-67006400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr11:67003800-67006400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:67003800-67006400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:67003800-67006400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr11:67004400-67006400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:67004600-67006400	Enhancers	Dnd41	blood
36	chr11:67005200-67006400	Enhancers	K562	blood
37	chr11:67005200-67007000	Enhancers	Liver	Liver
38	chr11:67005400-67006400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:67005400-67006400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:67005400-67006400	Weak transcription	Left Ventricle	heart
41	chr11:67005600-67006400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:67005600-67006400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:67005600-67006400	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr11:67005600-67006400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:67005600-67006400	Enhancers	Fetal Kidney	kidney
46	chr11:67005600-67006600	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr11:67005600-67006600	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr11:67005600-67006600	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr11:67005600-67006800	Enhancers	Fetal Intestine Large	intestine
50	chr11:67005600-67007000	Enhancers	Fetal Intestine Small	intestine

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