Variant report

Variant	rs2412338
Chromosome Location	chr11:3977521-3977522
allele	G/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	ZNF384	chr11:3977168-3977573	GM12878	blood:	n/a	n/a
2	MAFK	chr11:3977349-3977591	K562	blood:	n/a	chr11:3977450-3977465
3	MAFF	chr11:3977285-3977649	K562	blood:	n/a	chr11:3977448-3977466
4	MAFK	chr11:3977384-3977615	HepG2	liver:	n/a	chr11:3977450-3977465
5	MAFF	chr11:3977405-3977557	HepG2	liver:	n/a	chr11:3977448-3977466
6	EP300	chr11:3977380-3977580	K562	blood:	n/a	n/a
7	MAFK	chr11:3977419-3977582	HepG2	liver:	n/a	chr11:3977450-3977465

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3972776..3975865-chr11:3976108..3980315,4	K562	blood:
2	chr11:3975898..3977886-chr11:3979851..3982508,2	K562	blood:

Variant related genes	Relation type
ENSG00000255232	TF binding region
ENSG00000255232	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1013351	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs10500590	0.87[EUR][1000 genomes]
rs10742200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10767702	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs10767706	0.82[CHB][hapmap]
rs10767713	0.87[EUR][1000 genomes]
rs10767715	0.85[EUR][1000 genomes]
rs10767720	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767721	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10767723	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835311	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs10835312	0.83[EUR][1000 genomes]
rs10835320	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835324	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835331	0.80[CEU][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10835333	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835340	0.86[EUR][1000 genomes]
rs10835359	0.88[EUR][1000 genomes]
rs10835390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835399	0.87[EUR][1000 genomes]
rs10835402	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs10835403	0.86[EUR][1000 genomes]
rs10835406	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs10835407	0.87[EUR][1000 genomes]
rs10835508	0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs11030276	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs11030404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030599	0.81[EUR][1000 genomes]
rs11030639	0.81[EUR][1000 genomes]
rs11493482	0.81[EUR][1000 genomes]
rs1155146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11828337	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12223176	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs12270732	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12281293	0.87[EUR][1000 genomes]
rs12283447	0.87[EUR][1000 genomes]
rs12286710	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs12290747	0.85[EUR][1000 genomes]
rs12295138	0.81[EUR][1000 genomes]
rs1349583	0.88[EUR][1000 genomes]
rs1452047	0.87[EUR][1000 genomes]
rs1452048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17081	0.87[EUR][1000 genomes]
rs17279635	0.88[EUR][1000 genomes]
rs1839910	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898947	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs4910865	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910866	0.85[EUR][1000 genomes]
rs4910868	0.80[CEU][hapmap];0.88[EUR][1000 genomes]
rs4910869	0.82[EUR][1000 genomes]
rs6578421	0.82[YRI][hapmap]
rs6578424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66503725	0.88[EUR][1000 genomes]
rs66596383	0.90[EUR][1000 genomes]
rs67300156	0.86[EUR][1000 genomes]
rs7102215	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs7113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120938	0.82[CHB][hapmap]
rs7128762	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs720571	0.86[EUR][1000 genomes]
rs750525	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7924984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7925954	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7950153	0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs995498	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2412338	RRM1	cis	Thyroid	GTEx
rs2412338	STIM1	cis	lung	GTEx
rs2412338	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:67 , 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	chr11:3968200-3980200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:3969000-3980400	Weak transcription	NHLF	lung
4	chr11:3969400-3980000	Weak transcription	Liver	Liver
5	chr11:3969600-3977800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr11:3970600-3978000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:3970800-3977800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr11:3970800-3988600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr11:3971400-3988400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr11:3972800-3979400	Weak transcription	HepG2	liver
11	chr11:3972800-3979600	Weak transcription	A549	lung
12	chr11:3972800-3988800	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:3973000-3977800	Enhancers	Primary T cells from cord blood	blood
14	chr11:3973000-3978000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr11:3973000-3988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:3973200-3981000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:3973200-3982400	Weak transcription	Primary B cells from cord blood	blood
18	chr11:3973200-3984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:3973200-3993200	Weak transcription	Colon Smooth Muscle	Colon
20	chr11:3973200-4008400	Weak transcription	Fetal Lung	lung
21	chr11:3973600-3993800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:3973800-3979600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr11:3974200-3982200	Weak transcription	Brain Anterior Caudate	brain
24	chr11:3974400-3977800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr11:3974400-3980400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:3974400-3983400	Weak transcription	Small Intestine	intestine
27	chr11:3974600-3977600	Enhancers	HMEC	breast
28	chr11:3974800-3977800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:3974800-3979600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:3974800-3988200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr11:3974800-3988800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr11:3975000-4006000	Weak transcription	Right Ventricle	heart
33	chr11:3975200-3977600	Enhancers	NHEK	skin
34	chr11:3975400-3977600	Enhancers	Fetal Thymus	thymus
35	chr11:3975400-3979800	Weak transcription	Psoas Muscle	Psoas
36	chr11:3975600-3988600	Weak transcription	Dnd41	blood
37	chr11:3975600-3988800	Weak transcription	Aorta	Aorta
38	chr11:3975800-3978400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr11:3975800-3979200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:3975800-3984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:3975800-3988800	Weak transcription	Esophagus	oesophagus
42	chr11:3976000-3977800	Enhancers	GM12878-XiMat	blood
43	chr11:3976000-3980400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr11:3976200-3978800	Weak transcription	Thymus	Thymus
45	chr11:3976200-3979400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:3976200-3979600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:3976200-3979600	Weak transcription	Osteobl	bone
48	chr11:3976200-3980200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:3976200-3980200	Enhancers	K562	blood
50	chr11:3976400-3977800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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