Variant report

Variant	rs12223176
Chromosome Location	chr11:3982537-3982538
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1013351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10500590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10742200	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs10767702	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10767713	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10767715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10767767	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10767811	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10835239	0.82[CEU][hapmap]
rs10835311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835312	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835337	0.86[EUR][1000 genomes]
rs10835340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835359	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835390	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs10835399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835454	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835474	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835508	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10835521	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10835540	0.84[CEU][hapmap];0.94[CHB][hapmap]
rs10835556	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10835557	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10835561	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10835596	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835597	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835601	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835604	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11030276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11030404	0.88[EUR][1000 genomes]
rs11030579	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11030599	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11030627	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11030631	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11030639	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11030660	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11030781	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11493482	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1155146	0.81[CEU][hapmap]
rs11828337	0.86[EUR][1000 genomes]
rs12281293	1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12283447	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12286710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12290747	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12295138	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1349583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1442726	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1452047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1452048	0.87[EUR][1000 genomes]
rs17081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17279635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1839910	0.87[EUR][1000 genomes]
rs2119987	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412338	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs2898947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910590	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4910596	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4910597	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4910598	0.84[EUR][1000 genomes]
rs4910866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910869	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910875	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4910877	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4910880	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6578424	0.88[EUR][1000 genomes]
rs66503725	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66596383	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67065286	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67300156	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7102215	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7113845	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs7128762	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs714380	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71466139	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs720571	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7924984	0.88[EUR][1000 genomes]
rs7925954	0.84[EUR][1000 genomes]
rs7935824	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7950153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs963998	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs995498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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
rs12223176	RRM1	cis	Artery Tibial	GTEx
rs12223176	RRM1	cis	Thyroid	GTEx
rs12223176	STIM1	cis	lung	GTEx

Chromatin state (count:75 , 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	chr11:3979400-3982600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr11:3979400-3982600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr11:3979400-3983400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:3979600-3982600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:3979600-3982600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:3979600-3982600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr11:3979600-3982600	Enhancers	HMEC	breast
28	chr11:3979600-3982800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr11:3979600-3982800	Enhancers	NHDF-Ad	bronchial
30	chr11:3979800-3982600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr11:3979800-3982600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr11:3980200-3982600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr11:3980200-3982600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr11:3980400-3983400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr11:3980400-3984000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr11:3980600-3982800	Enhancers	Primary T cells from cord blood	blood
37	chr11:3980600-3984000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr11:3980600-3988800	Weak transcription	GM12878-XiMat	blood
39	chr11:3980600-3994200	Weak transcription	Fetal Stomach	stomach
40	chr11:3981000-3982600	Enhancers	HepG2	liver
41	chr11:3981000-3988800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:3981200-3983400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:3981200-3983400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:3981200-3983400	Weak transcription	Thymus	Thymus
45	chr11:3981200-3983400	Weak transcription	NHLF	lung
46	chr11:3981200-3984800	Weak transcription	K562	blood
47	chr11:3981200-3990400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:3981400-3982600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr11:3981400-3983800	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr11:3981400-3985200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links