Variant report

Variant	rs10835312
Chromosome Location	chr11:3950253-3950254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1013351	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10500590	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10742200	0.82[EUR][1000 genomes]
rs10767702	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767713	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767767	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10835311	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835331	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835337	0.86[EUR][1000 genomes]
rs10835340	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835359	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835390	0.83[EUR][1000 genomes]
rs10835399	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835402	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835403	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835406	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835407	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835454	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10835474	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10835508	0.82[EUR][1000 genomes]
rs10835556	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10835557	0.83[EUR][1000 genomes]
rs10835596	0.80[EUR][1000 genomes]
rs10835597	0.80[EUR][1000 genomes]
rs10835601	0.82[AMR][1000 genomes]
rs11030276	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11030404	0.83[EUR][1000 genomes]
rs11030579	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11030599	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11030627	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11030631	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11030639	0.83[EUR][1000 genomes]
rs11030660	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11493482	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11828337	0.82[EUR][1000 genomes]
rs12223176	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12281293	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12283447	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12286710	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12290747	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12295138	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1349583	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1442726	0.80[EUR][1000 genomes]
rs1452047	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1452048	0.85[EUR][1000 genomes]
rs17081	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17279635	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1839910	0.85[EUR][1000 genomes]
rs2412338	0.83[EUR][1000 genomes]
rs28419002	0.84[AFR][1000 genomes]
rs2898947	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910590	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910596	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4910597	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4910865	0.80[EUR][1000 genomes]
rs4910866	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910868	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910869	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4910875	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6578424	0.83[EUR][1000 genomes]
rs66503725	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66596383	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67065286	0.81[AMR][1000 genomes]
rs67300156	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102215	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7113845	0.82[EUR][1000 genomes]
rs7128762	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs714380	0.83[EUR][1000 genomes]
rs720571	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs750525	0.80[EUR][1000 genomes]
rs7924984	0.83[EUR][1000 genomes]
rs7935824	0.85[EUR][1000 genomes]
rs7950153	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs995498	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[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
rs10835312	STIM1	cis	lung	GTEx
rs10835312	RRM1	cis	Thyroid	GTEx
rs10835312	RRM1	cis	Artery Tibial	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	chr11:3939000-3956000	Weak transcription	Esophagus	oesophagus
7	chr11:3941600-3950600	Weak transcription	Stomach Mucosa	stomach
8	chr11:3941600-3951000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:3942000-3950400	Weak transcription	K562	blood
10	chr11:3942000-3950800	Weak transcription	Small Intestine	intestine
11	chr11:3942200-3951000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:3943200-3950400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:3943400-3954800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr11:3943800-3953200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr11:3944000-3950400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:3944000-3950800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr11:3947200-3952200	Enhancers	Liver	Liver
18	chr11:3947800-3950800	Weak transcription	HSMM	muscle
19	chr11:3948000-3950400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr11:3948000-3951400	Enhancers	Fetal Stomach	stomach
21	chr11:3948000-3952200	Enhancers	Fetal Muscle Leg	muscle
22	chr11:3948200-3955800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:3948200-3955800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:3948400-3950600	Weak transcription	Fetal Kidney	kidney
25	chr11:3948400-3951200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:3948400-3952800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr11:3948400-3960400	Weak transcription	NHEK	skin
28	chr11:3948600-3955600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:3948800-3950800	Weak transcription	HSMMtube	muscle
30	chr11:3948800-3951200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:3948800-3951400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:3948800-3954400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr11:3948800-3960800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:3949000-3950400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr11:3949000-3950600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:3949000-3950600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr11:3949000-3950800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr11:3949000-3950800	Weak transcription	A549	lung
39	chr11:3949000-3961400	Weak transcription	Right Atrium	heart
40	chr11:3949200-3950400	Weak transcription	HepG2	liver
41	chr11:3949200-3950600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:3949200-3950600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:3949200-3950800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:3949200-3954200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:3949400-3950400	Enhancers	Fetal Muscle Trunk	muscle
46	chr11:3949400-3950600	Weak transcription	Adipose Nuclei	Adipose
47	chr11:3949400-3950600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr11:3949400-3950600	Weak transcription	Thymus	Thymus
49	chr11:3949400-3951400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:3949400-3959400	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links