Variant report

Variant	rs11558445
Chromosome Location	chr21:46685175-46685176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46683847..46685633-chr4:13362055..13364820,2	MCF-7	breast:
2	chr21:46675525..46679390-chr21:46682642..46685767,4	MCF-7	breast:
3	chr21:46561382..46564170-chr21:46683644..46686214,2	MCF-7	breast:
4	chr21:46572711..46575083-chr21:46683577..46685513,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1056099	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1056100	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1056101	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11909411	0.88[ASN][1000 genomes]
rs13052344	0.87[ASN][1000 genomes]
rs2236443	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2236444	0.89[ASN][1000 genomes]
rs2236445	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2236446	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2236450	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2246697	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2255761	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255766	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2255774	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2256000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297283	0.93[AFR][1000 genomes]
rs2330102	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2330103	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838852	0.85[ASN][1000 genomes]
rs2838854	0.91[ASN][1000 genomes]
rs2838855	0.91[ASN][1000 genomes]
rs2838857	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2838858	0.91[ASN][1000 genomes]
rs2838859	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838860	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838861	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2838862	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838864	0.82[AMR][1000 genomes]
rs2838866	0.82[AMR][1000 genomes]
rs28442024	0.84[ASN][1000 genomes]
rs28501512	0.88[ASN][1000 genomes]
rs28576202	0.83[ASN][1000 genomes]
rs28616694	0.83[ASN][1000 genomes]
rs28622522	0.88[ASN][1000 genomes]
rs28623526	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28676615	0.87[ASN][1000 genomes]
rs34956478	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35776291	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35871601	0.83[ASN][1000 genomes]
rs3673	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4819050	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4819051	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4819053	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7275382	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7276591	0.87[ASN][1000 genomes]
rs7276828	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7279136	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7281263	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8127834	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8128636	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132135	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8134011	0.91[ASN][1000 genomes]
rs8134084	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs875620	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs875621	0.91[ASN][1000 genomes]
rs914214	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs914215	0.95[ASN][1000 genomes]
rs914218	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9974891	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9977686	0.85[ASN][1000 genomes]
rs9979545	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
9	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv916959	chr21:46585681-46831845	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
13	nsv1063721	chr21:46610599-46907894	Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv1059779	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
15	nsv544485	chr21:46611859-46891352	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
16	nsv1059805	chr21:46618210-46736943	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv913999	chr21:46636844-46765251	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
18	nsv914000	chr21:46647078-46765251	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
19	nsv914001	chr21:46647078-46944113	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
20	nsv914002	chr21:46655638-46945024	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
21	nsv1057807	chr21:46656346-47077374	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
22	nsv914003	chr21:46670874-46695039	Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv914004	chr21:46670874-46736694	Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
24	nsv914005	chr21:46670874-46756700	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
25	nsv914006	chr21:46670874-46788299	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
26	esv2762114	chr21:46680202-47067744	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
27	nsv914007	chr21:46684517-46780249	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
28	nsv914008	chr21:46684517-46792424	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
29	nsv914009	chr21:46684517-46908355	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11558445	LINC00315	cis	Artery Tibial	GTEx
rs11558445	LOC642852	Cis_1M	lymphoblastoid	RTeQTL
rs11558445	C21orf86	N/A	lymphoblastoid	RTeQTL
rs11558445	C21orf86	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46669200-46706600	Weak transcription	Right Atrium	heart
2	chr21:46675600-46686200	Weak transcription	GM12878-XiMat	blood
3	chr21:46676000-46706200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr21:46678800-46689800	Weak transcription	A549	lung
5	chr21:46679800-46687200	Weak transcription	Fetal Heart	heart
6	chr21:46680000-46689600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr21:46680600-46691400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:46680600-46700200	Weak transcription	Psoas Muscle	Psoas
9	chr21:46680800-46687000	Weak transcription	Fetal Brain Male	brain
10	chr21:46681000-46691800	Weak transcription	K562	blood
11	chr21:46681200-46687200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr21:46681400-46688000	Strong transcription	Stomach Smooth Muscle	stomach
13	chr21:46681400-46690200	Weak transcription	HUVEC	blood vessel
14	chr21:46681600-46685800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr21:46681600-46688000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr21:46681600-46688000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr21:46681600-46688000	Strong transcription	Fetal Stomach	stomach
18	chr21:46681600-46688000	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr21:46681800-46686200	Strong transcription	Spleen	Spleen
20	chr21:46681800-46686600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr21:46681800-46687400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr21:46681800-46687800	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr21:46681800-46688000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr21:46681800-46688000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr21:46681800-46688000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr21:46681800-46688000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr21:46681800-46688000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr21:46681800-46688000	Strong transcription	Brain Cingulate Gyrus	brain
29	chr21:46681800-46688000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr21:46681800-46688000	Strong transcription	Fetal Brain Female	brain
31	chr21:46681800-46688000	Strong transcription	Fetal Muscle Leg	muscle
32	chr21:46682000-46687800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr21:46682000-46687800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr21:46682000-46687800	Strong transcription	Brain Germinal Matrix	brain
35	chr21:46682000-46687800	Strong transcription	HSMMtube	muscle
36	chr21:46682000-46688000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr21:46682000-46688000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr21:46682000-46688000	Strong transcription	Brain Hippocampus Middle	brain
39	chr21:46682000-46688000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr21:46682200-46687800	Strong transcription	NHEK	skin
41	chr21:46682200-46688000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr21:46682200-46688000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr21:46682400-46687400	Strong transcription	Esophagus	oesophagus
44	chr21:46682400-46687800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr21:46682400-46687800	Strong transcription	Osteobl	bone
46	chr21:46682400-46688000	Strong transcription	Pancreas	Pancrea
47	chr21:46682600-46686000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr21:46682600-46686400	Strong transcription	Thymus	Thymus
49	chr21:46682600-46688000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr21:46682600-46697200	Weak transcription	Stomach Mucosa	stomach

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