Variant report

Variant	rs12295138
Chromosome Location	chr11:3932027-3932028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3924735..3926822-chr11:3929983..3932371,3	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1013351	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10500590	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10767702	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10767713	0.92[EUR][1000 genomes]
rs10767715	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10767767	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10835311	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10835312	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10835331	0.92[EUR][1000 genomes]
rs10835337	0.83[EUR][1000 genomes]
rs10835340	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10835359	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10835390	0.81[EUR][1000 genomes]
rs10835399	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10835402	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10835403	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10835406	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10835407	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10835454	0.81[EUR][1000 genomes]
rs10835474	0.84[EUR][1000 genomes]
rs10835557	0.80[EUR][1000 genomes]
rs11030276	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11030404	0.81[EUR][1000 genomes]
rs11030579	0.82[EUR][1000 genomes]
rs11030599	0.84[EUR][1000 genomes]
rs11030627	0.81[EUR][1000 genomes]
rs11030631	0.82[EUR][1000 genomes]
rs11030639	0.80[EUR][1000 genomes]
rs11030660	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11493482	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12223176	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12281293	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12283447	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12286710	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12286851	0.82[ASN][1000 genomes]
rs12290747	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1349583	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1452047	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1452048	0.82[EUR][1000 genomes]
rs17081	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17279635	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1839910	0.82[EUR][1000 genomes]
rs2119987	0.89[AFR][1000 genomes]
rs2412338	0.81[EUR][1000 genomes]
rs2898947	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4910590	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4910866	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4910868	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4910869	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4910875	0.83[EUR][1000 genomes]
rs6578424	0.81[EUR][1000 genomes]
rs66503725	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66596383	0.90[EUR][1000 genomes]
rs67300156	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7102215	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7128762	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs714380	0.81[EUR][1000 genomes]
rs720571	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7924984	0.81[EUR][1000 genomes]
rs7935824	0.82[EUR][1000 genomes]
rs7950153	0.93[EUR][1000 genomes]
rs963998	0.89[AFR][1000 genomes]
rs995498	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv1051904	chr11:3903226-3939186	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1050077	chr11:3903226-3940726	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12295138	RRM1	cis	Thyroid	GTEx
rs12295138	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3916600-3943800	Weak transcription	Fetal Stomach	stomach
2	chr11:3916600-3948800	Weak transcription	Aorta	Aorta
3	chr11:3924000-3950600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr11:3924200-3934400	Weak transcription	Gastric	stomach
5	chr11:3924800-3938200	Weak transcription	Pancreas	Pancrea
6	chr11:3925800-3941000	Weak transcription	Right Ventricle	heart
7	chr11:3926600-3938400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:3926600-3941000	Weak transcription	Small Intestine	intestine
9	chr11:3926800-3937000	Weak transcription	Lung	lung
10	chr11:3927200-3933200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:3927200-3936000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:3927200-3942600	Weak transcription	Spleen	Spleen
13	chr11:3927400-3941200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr11:3927600-3943600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr11:3928400-3940800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:3928800-3938200	Weak transcription	A549	lung
17	chr11:3929000-3938200	Weak transcription	Esophagus	oesophagus
18	chr11:3929200-3932400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:3929200-3932800	Weak transcription	Primary T cells from cord blood	blood
20	chr11:3929200-3934200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:3929200-3934400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:3929200-3935400	Weak transcription	Primary B cells from cord blood	blood
23	chr11:3929200-3935600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr11:3929200-3936000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr11:3929200-3937200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:3929200-3938200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr11:3929200-3940800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:3929400-3932200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:3929400-3932200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:3929400-3937200	Weak transcription	Dnd41	blood
31	chr11:3929400-3937400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:3929400-3938200	Weak transcription	GM12878-XiMat	blood
33	chr11:3929400-3950600	Weak transcription	Ovary	ovary
34	chr11:3930200-3932400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr11:3930200-3938000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:3930400-3932600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr11:3930400-3932600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr11:3930400-3933000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:3930400-3934600	Weak transcription	HepG2	liver
40	chr11:3930400-3936000	Weak transcription	HMEC	breast
41	chr11:3930400-3937000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr11:3930400-3937400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:3930600-3932200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:3930600-3936000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr11:3930600-3938200	Weak transcription	Psoas Muscle	Psoas
46	chr11:3930600-3940800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:3930800-3932200	Weak transcription	Fetal Thymus	thymus
48	chr11:3930800-3932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr11:3931400-3933200	Enhancers	K562	blood
50	chr11:3931400-3934000	Weak transcription	Liver	Liver

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