Variant report

Variant	rs3741189
Chromosome Location	chr11:66995603-66995604
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	POLR2A	chr11:66995575-66995719	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
KDM2A	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10400320	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10732253	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]
rs10750796	1.00[AFR][1000 genomes];1.00[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];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1894111	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]
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];0.82[YRI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4271388	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4344498	1.00[AFR][1000 genomes];1.00[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];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57327069	0.81[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];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs655168	0.84[AFR][1000 genomes];0.86[AMR][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];0.96[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][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];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[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
rs3741189	RPS6KB2	cis	multi-tissue	Pritchard
rs3741189	RPS6KB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66936400-67006200	Weak transcription	Stomach Mucosa	stomach
2	chr11:66956400-67005000	Weak transcription	Fetal Heart	heart
3	chr11:66962200-66999000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:66964600-67002400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:66965200-67006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:66972800-67002600	Strong transcription	Fetal Muscle Trunk	muscle
7	chr11:66973000-67005400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:66974800-66997600	Strong transcription	Fetal Thymus	thymus
9	chr11:66980400-67002200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:66980800-67005600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:66981000-67003800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:66981600-67005200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:66981800-67006400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:66982000-66997800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:66982000-67005800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr11:66982400-67003800	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:66982800-67002600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:66982800-67002600	Strong transcription	Adipose Nuclei	Adipose
19	chr11:66987000-67006000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:66987800-66995800	Weak transcription	Aorta	Aorta
21	chr11:66988400-66999000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:66989200-66998400	Weak transcription	Small Intestine	intestine
23	chr11:66990200-67002200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:66990400-66997600	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr11:66990400-67002200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:66990400-67003400	Strong transcription	Fetal Muscle Leg	muscle
27	chr11:66990400-67004400	Strong transcription	Fetal Stomach	stomach
28	chr11:66990400-67005200	Strong transcription	Fetal Intestine Small	intestine
29	chr11:66990600-66996600	Strong transcription	Primary T cells from cord blood	blood
30	chr11:66990800-66997000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:66990800-66999400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:66990800-67000200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:66990800-67000400	Strong transcription	Placenta	Placenta
34	chr11:66990800-67002400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:66990800-67005400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:66991000-66996800	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:66991000-66999600	Strong transcription	HSMMtube	muscle
38	chr11:66991000-67000000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:66991000-67000600	Strong transcription	Thymus	Thymus
40	chr11:66991000-67002400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:66991000-67002400	Strong transcription	Fetal Intestine Large	intestine
42	chr11:66991200-67001200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:66991400-66999400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr11:66991400-67000000	Strong transcription	Stomach Smooth Muscle	stomach
45	chr11:66993200-66995800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr11:66994200-66997600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr11:66994200-66999600	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr11:66994200-66999800	Strong transcription	Hela-S3	cervix
49	chr11:66994200-67002000	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:66994400-66997000	Strong transcription	K562	blood

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