Variant report

Variant	rs1839910
Chromosome Location	chr11:3966722-3966723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1013351	0.86[EUR][1000 genomes]
rs10500590	0.88[EUR][1000 genomes]
rs10742200	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10767702	0.86[EUR][1000 genomes]
rs10767713	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10767715	0.86[EUR][1000 genomes]
rs10767720	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767721	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10767723	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835311	0.86[EUR][1000 genomes]
rs10835312	0.85[EUR][1000 genomes]
rs10835320	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835324	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835331	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10835333	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835337	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835340	0.87[EUR][1000 genomes]
rs10835359	0.87[EUR][1000 genomes]
rs10835390	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835399	0.86[EUR][1000 genomes]
rs10835402	0.86[EUR][1000 genomes]
rs10835403	0.85[EUR][1000 genomes]
rs10835406	0.86[EUR][1000 genomes]
rs10835407	0.86[EUR][1000 genomes]
rs11030276	0.86[EUR][1000 genomes]
rs11030404	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11030599	0.80[EUR][1000 genomes]
rs11030639	0.80[EUR][1000 genomes]
rs11828337	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12223176	0.87[EUR][1000 genomes]
rs12270732	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12281293	0.88[EUR][1000 genomes]
rs12283447	0.86[EUR][1000 genomes]
rs12286710	0.88[EUR][1000 genomes]
rs12290747	0.86[EUR][1000 genomes]
rs12295138	0.82[EUR][1000 genomes]
rs1349583	0.87[EUR][1000 genomes]
rs1452047	0.86[EUR][1000 genomes]
rs1452048	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17081	0.86[EUR][1000 genomes]
rs17279635	0.87[EUR][1000 genomes]
rs2412338	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898947	0.87[EUR][1000 genomes]
rs4910865	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910866	0.86[EUR][1000 genomes]
rs4910868	0.87[EUR][1000 genomes]
rs4910869	0.81[EUR][1000 genomes]
rs6578424	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66503725	0.87[EUR][1000 genomes]
rs66596383	0.89[EUR][1000 genomes]
rs67300156	0.87[EUR][1000 genomes]
rs7102215	0.86[EUR][1000 genomes]
rs7113845	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7128762	0.86[EUR][1000 genomes]
rs720571	0.85[EUR][1000 genomes]
rs750525	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7924984	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7925954	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7950153	0.88[EUR][1000 genomes]
rs995498	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
rs1839910	STIM1	cis	lung	GTEx
rs1839910	RRM1	cis	Artery Tibial	GTEx
rs1839910	RRM1	cis	Thyroid	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3950400-3972200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr11:3951200-3967600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr11:3958800-3968000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr11:3960000-3967600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr11:3960200-3967600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr11:3961200-4002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:3961400-3968600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:3961400-3968600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr11:3961400-3969200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:3961600-3967600	Weak transcription	Brain Angular Gyrus	brain
11	chr11:3961600-3967800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:3961600-3968000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:3961600-3968400	Weak transcription	NHEK	skin
14	chr11:3961600-3975200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:3961800-3968000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:3962000-3971800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr11:3962000-3973400	Weak transcription	Ovary	ovary
18	chr11:3962400-3968000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr11:3962400-3968400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr11:3962600-3968200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:3963000-3967000	Enhancers	Fetal Thymus	thymus
22	chr11:3963000-3968600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:3963000-3973200	Enhancers	Primary B cells from peripheral blood	blood
24	chr11:3963200-3967800	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr11:3963200-3968400	Enhancers	Primary hematopoietic stem cells	blood
26	chr11:3963400-3966800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr11:3963400-3969400	Enhancers	Adipose Nuclei	Adipose
28	chr11:3963400-3969400	Enhancers	Left Ventricle	heart
29	chr11:3963600-3967800	Weak transcription	Colonic Mucosa	Colon
30	chr11:3963800-3967200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr11:3964200-3967000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:3964200-3967800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:3964200-3968000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr11:3964200-3968000	Weak transcription	Placenta	Placenta
35	chr11:3964400-3968000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr11:3964400-3968000	Weak transcription	Lung	lung
37	chr11:3964400-3968400	Enhancers	Primary T cells fromperipheralblood	blood
38	chr11:3964400-3968600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr11:3964400-3971600	Weak transcription	A549	lung
40	chr11:3964400-3972000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:3964400-3972400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:3964600-3967800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr11:3964600-3968000	Weak transcription	Fetal Kidney	kidney
44	chr11:3964600-3970000	Weak transcription	K562	blood
45	chr11:3964800-3967200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr11:3964800-3967400	Enhancers	Primary T cells from cord blood	blood
47	chr11:3964800-3967400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr11:3964800-3967800	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr11:3964800-3968000	Weak transcription	HMEC	breast
50	chr11:3965000-3967000	Weak transcription	Primary B cells from cord blood	blood

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