Variant report

Variant	rs10835311
Chromosome Location	chr11:3949027-3949028
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3941075..3946343-chr11:3946471..3949436,5	K562	blood:
2	chr11:3948392..3949376-chr11:4093449..4094397,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206976	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1013351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10742200	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs10767702	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767713	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767720	0.81[EUR][1000 genomes]
rs10767721	0.81[EUR][1000 genomes]
rs10767723	0.81[EUR][1000 genomes]
rs10767767	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10767811	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10835239	0.82[CEU][hapmap]
rs10835312	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835324	0.81[EUR][1000 genomes]
rs10835331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835333	0.81[EUR][1000 genomes]
rs10835337	0.87[EUR][1000 genomes]
rs10835340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835359	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835390	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs10835399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835454	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10835474	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10835508	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10835521	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10835540	0.84[CEU][hapmap];0.94[CHB][hapmap]
rs10835556	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10835557	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10835561	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10835596	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs10835597	0.81[EUR][1000 genomes]
rs10835601	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs10835604	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11030276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11030404	0.85[EUR][1000 genomes]
rs11030579	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11030599	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11030627	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11030631	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11030639	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11030660	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11030781	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11493482	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1155146	0.81[CEU][hapmap]
rs11828337	0.83[EUR][1000 genomes]
rs12223176	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]
rs12270732	0.81[EUR][1000 genomes]
rs12281293	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12283447	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12286710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12290747	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12295138	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1349583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1442726	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1452047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1452048	0.86[EUR][1000 genomes]
rs17081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17279635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1839910	0.86[EUR][1000 genomes]
rs2412338	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs28419002	0.84[AFR][1000 genomes]
rs2898947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910590	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910596	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4910597	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4910598	0.81[EUR][1000 genomes]
rs4910865	0.82[EUR][1000 genomes]
rs4910866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910869	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4910875	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4910877	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4910880	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6578424	0.85[EUR][1000 genomes]
rs66503725	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66596383	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67065286	0.82[AMR][1000 genomes]
rs67300156	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102215	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7113845	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs7128762	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs714380	0.84[EUR][1000 genomes]
rs718937	1.00[YRI][hapmap]
rs720571	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs750525	0.82[EUR][1000 genomes]
rs7924984	0.85[EUR][1000 genomes]
rs7925954	0.81[EUR][1000 genomes]
rs7935824	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7950153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963998	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs995498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv1043039	chr11:3903226-3955159	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv896895	chr11:3942001-3972236	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10835311	STIM1	cis	lung	GTEx
rs10835311	RRM1	cis	Artery Tibial	GTEx
rs10835311	RRM1	cis	Thyroid	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3924000-3950600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:3929400-3950600	Weak transcription	Ovary	ovary
3	chr11:3934800-3951000	Weak transcription	Gastric	stomach
4	chr11:3937800-3950600	Weak transcription	Lung	lung
5	chr11:3938400-3956400	Weak transcription	Dnd41	blood
6	chr11:3938600-3949800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:3939000-3950200	Weak transcription	Left Ventricle	heart
8	chr11:3939000-3950200	Weak transcription	Pancreas	Pancrea
9	chr11:3939000-3956000	Weak transcription	Esophagus	oesophagus
10	chr11:3939600-3950000	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:3939600-3950200	Weak transcription	Fetal Thymus	thymus
12	chr11:3941600-3950600	Weak transcription	Stomach Mucosa	stomach
13	chr11:3941600-3951000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:3942000-3950200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:3942000-3950400	Weak transcription	K562	blood
16	chr11:3942000-3950800	Weak transcription	Small Intestine	intestine
17	chr11:3942200-3951000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:3943200-3949800	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr11:3943200-3950400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr11:3943400-3949800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr11:3943400-3954800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:3943800-3953200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr11:3944000-3950400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr11:3944000-3950800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr11:3947200-3952200	Enhancers	Liver	Liver
26	chr11:3947400-3949200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:3947400-3949200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:3947400-3949200	Enhancers	Psoas Muscle	Psoas
29	chr11:3947400-3949400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr11:3947600-3950000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr11:3947800-3949200	Enhancers	HepG2	liver
32	chr11:3947800-3949400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr11:3947800-3949400	Enhancers	Fetal Lung	lung
34	chr11:3947800-3949400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr11:3947800-3949600	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr11:3947800-3950200	Enhancers	Primary B cells from peripheral blood	blood
37	chr11:3947800-3950800	Weak transcription	HSMM	muscle
38	chr11:3948000-3949200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr11:3948000-3949800	Enhancers	Primary B cells from cord blood	blood
40	chr11:3948000-3950400	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr11:3948000-3951400	Enhancers	Fetal Stomach	stomach
42	chr11:3948000-3952200	Enhancers	Fetal Muscle Leg	muscle
43	chr11:3948200-3955800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:3948200-3955800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:3948400-3950600	Weak transcription	Fetal Kidney	kidney
46	chr11:3948400-3951200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:3948400-3952800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr11:3948400-3960400	Weak transcription	NHEK	skin
49	chr11:3948600-3949200	Enhancers	Right Ventricle	heart
50	chr11:3948600-3949800	Weak transcription	Fetal Heart	heart

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