Variant report

Variant	rs1013351
Chromosome Location	chr11:3952303-3952304
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:3946137..3948260-chr11:3950901..3953972,3	MCF-7	breast:
2	chr11:3952025..3954655-chr11:3956750..3959173,2	MCF-7	breast:
3	chr11:3860976..3863338-chr11:3950724..3953405,2	K562	blood:

Variant related genes	Relation type
ENSG00000177105	Chromatin interaction

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

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

rs_ID	r²[population]
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];0.84[EUR][1000 genomes]
rs10767702	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767720	0.82[EUR][1000 genomes]
rs10767721	0.82[EUR][1000 genomes]
rs10767723	0.81[EUR][1000 genomes]
rs10767767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10767811	0.83[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10835239	0.82[CEU][hapmap]
rs10835311	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]
rs10835312	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[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	0.80[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];0.96[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];0.96[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];0.96[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];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10835454	0.85[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	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10835521	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10835540	0.87[CEU][hapmap];0.93[CHB][hapmap]
rs10835556	0.95[CEU][hapmap];0.93[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	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10835596	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10835597	0.82[EUR][1000 genomes]
rs10835601	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs10835604	0.91[CEU][hapmap];0.93[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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11030404	0.85[EUR][1000 genomes]
rs11030579	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11030599	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11030627	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11030631	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11030639	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11030660	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11030781	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11493482	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1155146	0.80[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];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12270732	0.82[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];0.96[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];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12290747	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12295138	0.90[AMR][1000 genomes];0.95[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	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[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];0.96[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];0.96[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];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1839910	0.86[EUR][1000 genomes]
rs2412338	0.80[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];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910590	0.85[AMR][1000 genomes];0.87[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	0.81[EUR][1000 genomes]
rs4910866	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[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];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910869	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4910875	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4910877	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4910880	0.82[CEU][hapmap];0.92[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];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66596383	0.89[AMR][1000 genomes];0.95[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];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7113845	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs7128762	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs714380	0.85[EUR][1000 genomes]
rs718937	1.00[YRI][hapmap]
rs720571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs750525	0.81[EUR][1000 genomes]
rs7924984	0.85[EUR][1000 genomes]
rs7925954	0.81[EUR][1000 genomes]
rs7935824	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7950153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963998	0.91[CEU][hapmap];0.93[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
rs1013351	RRM1	cis	Artery Tibial	GTEx
rs1013351	RRM1	cis	Thyroid	GTEx
rs1013351	STIM1	cis	lung	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3938400-3956400	Weak transcription	Dnd41	blood
2	chr11:3939000-3956000	Weak transcription	Esophagus	oesophagus
3	chr11:3943400-3954800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:3943800-3953200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr11:3948200-3955800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:3948200-3955800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:3948400-3952800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:3948400-3960400	Weak transcription	NHEK	skin
9	chr11:3948600-3955600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:3948800-3954400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr11:3948800-3960800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:3949000-3961400	Weak transcription	Right Atrium	heart
13	chr11:3949200-3954200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr11:3949400-3959400	Weak transcription	Fetal Lung	lung
15	chr11:3949600-3953600	Strong transcription	Primary T cells from cord blood	blood
16	chr11:3949800-3952600	Enhancers	Fetal Heart	heart
17	chr11:3950000-3953000	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr11:3950000-3957600	Weak transcription	GM12878-XiMat	blood
19	chr11:3950200-3953600	Enhancers	Psoas Muscle	Psoas
20	chr11:3950400-3952400	Enhancers	HepG2	liver
21	chr11:3950400-3972200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr11:3950600-3953000	Strong transcription	Primary B cells from cord blood	blood
23	chr11:3950800-3956200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr11:3951000-3954600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:3951000-3955600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr11:3951000-3957400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr11:3951000-3960600	Weak transcription	Stomach Mucosa	stomach
28	chr11:3951200-3952800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:3951200-3953600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr11:3951200-3954800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:3951200-3965400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:3951200-3967600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:3951400-3952600	Weak transcription	Ovary	ovary
34	chr11:3951400-3952600	Enhancers	Stomach Smooth Muscle	stomach
35	chr11:3951400-3952600	Weak transcription	Thymus	Thymus
36	chr11:3951400-3952800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr11:3951400-3953000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:3951400-3953200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr11:3951400-3953200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr11:3951400-3954000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr11:3951400-3955000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr11:3951400-3955600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr11:3951400-3955800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr11:3951400-3955800	Weak transcription	Fetal Stomach	stomach
45	chr11:3951400-3956000	Weak transcription	Aorta	Aorta
46	chr11:3951400-3956000	Weak transcription	Gastric	stomach
47	chr11:3951400-3956400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr11:3951400-3959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr11:3951400-3959200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:3951400-3959800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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