Variant report

Variant	rs66596383
Chromosome Location	chr11:3979745-3979746
allele	C/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	CTCF	chr11:3979600-3979750	AG04449	skin:	n/a	chr11:3979681-3979699 chr11:3979683-3979696
2	CTCF	chr11:3979700-3979850	AG04449	skin:	n/a	n/a
3	CTCF	chr11:3979695-3979745	K562	blood:	n/a	n/a
4	CTCF	chr11:3979737-3979745	GM10248	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3979407..3982038-chr11:3982601..3985547,3	K562	blood:
2	chr11:3972776..3975865-chr11:3976108..3980315,4	K562	blood:

Variant related genes	Relation type
ENSG00000255232	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1013351	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10500590	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10742200	0.89[EUR][1000 genomes]
rs10767702	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10767713	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767715	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767720	0.81[EUR][1000 genomes]
rs10767721	0.81[EUR][1000 genomes]
rs10767723	0.81[EUR][1000 genomes]
rs10767767	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10835311	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835312	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835324	0.81[EUR][1000 genomes]
rs10835331	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835333	0.81[EUR][1000 genomes]
rs10835337	0.88[EUR][1000 genomes]
rs10835340	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835359	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835390	0.90[EUR][1000 genomes]
rs10835399	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835402	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835403	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835406	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835407	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835454	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835474	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835508	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10835556	0.84[EUR][1000 genomes]
rs10835557	0.85[EUR][1000 genomes]
rs10835596	0.82[EUR][1000 genomes]
rs10835597	0.82[EUR][1000 genomes]
rs10835601	0.80[EUR][1000 genomes]
rs11030276	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11030404	0.90[EUR][1000 genomes]
rs11030579	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11030599	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11030627	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11030631	0.87[EUR][1000 genomes]
rs11030639	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11030660	0.88[EUR][1000 genomes]
rs11493482	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11827795	0.85[AFR][1000 genomes]
rs11828337	0.88[EUR][1000 genomes]
rs12223176	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12270732	0.81[EUR][1000 genomes]
rs12281293	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12283447	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12286710	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12290747	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12295138	0.90[EUR][1000 genomes]
rs1349583	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442726	0.82[EUR][1000 genomes]
rs1452047	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1452048	0.89[EUR][1000 genomes]
rs17081	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17279635	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1839910	0.89[EUR][1000 genomes]
rs2412338	0.90[EUR][1000 genomes]
rs2898947	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910590	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4910596	0.83[EUR][1000 genomes]
rs4910597	0.83[EUR][1000 genomes]
rs4910598	0.82[EUR][1000 genomes]
rs4910865	0.80[EUR][1000 genomes]
rs4910866	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4910868	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910869	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4910875	0.88[EUR][1000 genomes]
rs57365434	0.82[AFR][1000 genomes]
rs6578424	0.90[EUR][1000 genomes]
rs66503725	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67300156	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7102215	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7113845	0.89[EUR][1000 genomes]
rs7128762	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs714380	0.86[EUR][1000 genomes]
rs71466139	0.83[ASN][1000 genomes]
rs720571	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs750525	0.80[EUR][1000 genomes]
rs7924984	0.90[EUR][1000 genomes]
rs7925954	0.86[EUR][1000 genomes]
rs7935824	0.87[EUR][1000 genomes]
rs7938862	0.84[AFR][1000 genomes]
rs7950153	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs995498	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][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
rs66596383	RRM1	cis	Thyroid	GTEx
rs66596383	RRM1	cis	Artery Tibial	GTEx
rs66596383	STIM1	cis	lung	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	chr11:3970800-3988600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr11:3971400-3988400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr11:3972800-3988800	Weak transcription	Fetal Muscle Leg	muscle
8	chr11:3973000-3988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:3973200-3981000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:3973200-3982400	Weak transcription	Primary B cells from cord blood	blood
11	chr11:3973200-3984800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:3973200-3993200	Weak transcription	Colon Smooth Muscle	Colon
13	chr11:3973200-4008400	Weak transcription	Fetal Lung	lung
14	chr11:3973600-3993800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr11:3974200-3982200	Weak transcription	Brain Anterior Caudate	brain
16	chr11:3974400-3980400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:3974400-3983400	Weak transcription	Small Intestine	intestine
18	chr11:3974800-3988200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr11:3974800-3988800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr11:3975000-4006000	Weak transcription	Right Ventricle	heart
21	chr11:3975400-3979800	Weak transcription	Psoas Muscle	Psoas
22	chr11:3975600-3988600	Weak transcription	Dnd41	blood
23	chr11:3975600-3988800	Weak transcription	Aorta	Aorta
24	chr11:3975800-3984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:3975800-3988800	Weak transcription	Esophagus	oesophagus
26	chr11:3976000-3980400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr11:3976200-3980200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:3976200-3980200	Enhancers	K562	blood
29	chr11:3977200-3982200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:3977400-3980200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr11:3977400-3983000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr11:3977400-3985400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:3977400-3988600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr11:3977600-3980400	Weak transcription	Fetal Thymus	thymus
35	chr11:3977600-3980600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr11:3977800-3979800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr11:3977800-3980200	Weak transcription	GM12878-XiMat	blood
38	chr11:3977800-3980600	Weak transcription	Primary T cells from cord blood	blood
39	chr11:3977800-3981400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr11:3977800-3982200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:3978000-3979800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:3978400-3980200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr11:3978600-3980400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr11:3979000-3981200	Enhancers	Placenta	Placenta
45	chr11:3979200-3980200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr11:3979400-3980400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:3979400-3980400	Enhancers	HepG2	liver
48	chr11:3979400-3981000	Enhancers	Primary T cells fromperipheralblood	blood
49	chr11:3979400-3981800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:3979400-3982000	Enhancers	NHEK	skin

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