Variant report

Variant	rs7925954
Chromosome Location	chr11:3982746-3982747
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3979407..3982038-chr11:3982601..3985547,3	K562	blood:
2	chr11:3973583..3975273-chr11:3982575..3984995,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RRM1-8	chr11:3982507-3982768	NONHSAT017631

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1013351	0.81[EUR][1000 genomes]
rs10500590	0.83[EUR][1000 genomes]
rs10742200	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10767702	0.81[EUR][1000 genomes]
rs10767713	0.82[EUR][1000 genomes]
rs10767715	0.81[EUR][1000 genomes]
rs10767720	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10767721	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10767723	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10835311	0.81[EUR][1000 genomes]
rs10835320	0.94[AMR][1000 genomes]
rs10835324	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10835331	0.83[EUR][1000 genomes]
rs10835333	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835337	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10835340	0.82[EUR][1000 genomes]
rs10835359	0.83[EUR][1000 genomes]
rs10835390	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835399	0.83[EUR][1000 genomes]
rs10835402	0.83[EUR][1000 genomes]
rs10835403	0.82[EUR][1000 genomes]
rs10835406	0.83[EUR][1000 genomes]
rs10835407	0.83[EUR][1000 genomes]
rs11030276	0.81[EUR][1000 genomes]
rs11030404	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11828337	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12223176	0.84[EUR][1000 genomes]
rs12270732	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12281293	0.83[EUR][1000 genomes]
rs12283447	0.83[EUR][1000 genomes]
rs12286710	0.82[EUR][1000 genomes]
rs12290747	0.81[EUR][1000 genomes]
rs1349583	0.83[EUR][1000 genomes]
rs1452047	0.83[EUR][1000 genomes]
rs1452048	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17081	0.83[EUR][1000 genomes]
rs17279635	0.84[EUR][1000 genomes]
rs1839910	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412338	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2898947	0.84[EUR][1000 genomes]
rs4910865	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4910866	0.81[EUR][1000 genomes]
rs4910868	0.84[EUR][1000 genomes]
rs6578424	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66503725	0.84[EUR][1000 genomes]
rs66596383	0.86[EUR][1000 genomes]
rs67300156	0.82[EUR][1000 genomes]
rs7102215	0.81[EUR][1000 genomes]
rs7113845	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7128762	0.81[EUR][1000 genomes]
rs720571	0.82[EUR][1000 genomes]
rs750525	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7924984	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7950153	0.82[EUR][1000 genomes]
rs995498	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2586241	chr11:3981859-3983419	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3468274	chr11:3982275-3982933	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3394565	chr11:3982277-3983005	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2151404	chr11:3982291-3983047	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv3516459	chr11:3982297-3982911	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv3516460	chr11:3982302-3983004	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv3468286	chr11:3982356-3982876	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3516461	chr11:3982356-3982876	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7925954	RRM1	cis	Thyroid	GTEx
rs7925954	RRM1	cis	Artery Tibial	GTEx
rs7925954	STIM1	cis	lung	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3961200-4002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:3970800-3988600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr11:3971400-3988400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:3972800-3988800	Weak transcription	Fetal Muscle Leg	muscle
5	chr11:3973000-3988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:3973200-3984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:3973200-3993200	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:3973200-4008400	Weak transcription	Fetal Lung	lung
9	chr11:3973600-3993800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:3974400-3983400	Weak transcription	Small Intestine	intestine
11	chr11:3974800-3988200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr11:3974800-3988800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:3975000-4006000	Weak transcription	Right Ventricle	heart
14	chr11:3975600-3988600	Weak transcription	Dnd41	blood
15	chr11:3975600-3988800	Weak transcription	Aorta	Aorta
16	chr11:3975800-3984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:3975800-3988800	Weak transcription	Esophagus	oesophagus
18	chr11:3977400-3983000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr11:3977400-3985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:3977400-3988600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr11:3979400-3983400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:3979600-3982800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr11:3979600-3982800	Enhancers	NHDF-Ad	bronchial
24	chr11:3980400-3983400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr11:3980400-3984000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr11:3980600-3982800	Enhancers	Primary T cells from cord blood	blood
27	chr11:3980600-3984000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr11:3980600-3988800	Weak transcription	GM12878-XiMat	blood
29	chr11:3980600-3994200	Weak transcription	Fetal Stomach	stomach
30	chr11:3981000-3988800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:3981200-3983400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:3981200-3983400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr11:3981200-3983400	Weak transcription	Thymus	Thymus
34	chr11:3981200-3983400	Weak transcription	NHLF	lung
35	chr11:3981200-3984800	Weak transcription	K562	blood
36	chr11:3981200-3990400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:3981400-3983800	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr11:3981400-3985200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:3981600-3988800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:3981600-3993000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:3981800-3989800	Weak transcription	Osteobl	bone
42	chr11:3981800-3990800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:3982000-3983400	Weak transcription	Liver	Liver
44	chr11:3982000-3983400	Weak transcription	A549	lung
45	chr11:3982000-3984400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr11:3982000-3993200	Weak transcription	NHEK	skin
47	chr11:3982200-3988800	Weak transcription	Spleen	Spleen
48	chr11:3982400-3983400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:3982400-3983400	Weak transcription	Lung	lung
50	chr11:3982400-3983800	Weak transcription	Adipose Nuclei	Adipose

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