Variant report

Variant	rs1892693
Chromosome Location	chr21:47967477-47967478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47962897..47964618-chr21:47964925..47967563,2	K562	blood:
2	chr21:47966167..47967910-chr21:47973256..47975447,2	MCF-7	breast:
3	chr21:47964144..47967545-chr21:47972969..47977002,4	K562	blood:
4	chr21:47961062..47963795-chr21:47966527..47968756,2	MCF-7	breast:
5	chr21:47966998..47969983-chr21:47970602..47975589,5	MCF-7	breast:
6	chr17:59415209..59417169-chr21:47966964..47969396,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160305	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11508685	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16979254	0.93[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839252	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2839264	1.00[ASN][1000 genomes]
rs2839266	1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2839303	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839315	1.00[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839316	1.00[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839340	0.82[YRI][hapmap]
rs55878170	1.00[ASN][1000 genomes]
rs56034615	1.00[ASN][1000 genomes]
rs7283507	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73146739	1.00[ASN][1000 genomes]
rs73148704	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73152856	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73152858	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
2	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
3	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
4	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
5	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
6	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
7	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
8	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
9	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
10	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
11	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
12	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
13	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
14	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
15	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
16	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
17	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
18	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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	30 gene(s)	inside rSNPs	n/a
19	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
20	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
21	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
22	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
23	nsv1059466	chr21:47894705-48096945	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
24	nsv1061185	chr21:47901250-48096945	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
25	nsv1057566	chr21:47915583-48029698	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	n/a
26	nsv587999	chr21:47941916-48103851	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
27	nsv1058589	chr21:47948030-48091343	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
28	nsv1057643	chr21:47953820-48056600	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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 target site	36 gene(s)	inside rSNPs	n/a
29	nsv544497	chr21:47953820-48056600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	n/a
30	nsv914147	chr21:47958657-47982652	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
31	nsv459313	chr21:47964259-47982652	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
32	nsv588000	chr21:47964259-47982652	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
33	nsv588001	chr21:47966504-47986001	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1892693	C21orf57	Cis_1M	lymphoblastoid	RTeQTL
rs1892693	SPATC1L	cis	Adipose Subcutaneous	GTEx
rs1892693	SPATC1L	cis	Thyroid	GTEx
rs1892693	C21orf56	cis	multi-tissue	Pritchard
rs1892693	SPATC1L	cis	lung	GTEx
rs1892693	C21orf56	cis	lymphoblastoid	seeQTL
rs1892693	SPATC1L	cis	Esophagus Mucosa	GTEx
rs1892693	SPATC1L	cis	Muscle Skeletal	GTEx
rs1892693	SPATC1L	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47943600-47990600	Strong transcription	Fetal Stomach	stomach
2	chr21:47947200-47975200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr21:47947600-47989000	Strong transcription	Dnd41	blood
4	chr21:47947600-47991000	Strong transcription	Fetal Muscle Leg	muscle
5	chr21:47948000-47968400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr21:47948400-47971600	Strong transcription	Fetal Muscle Trunk	muscle
7	chr21:47948400-47993600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr21:47948600-47968000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr21:47948600-47968000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr21:47948600-47971400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr21:47948600-47993200	Strong transcription	Fetal Intestine Large	intestine
12	chr21:47948800-47969000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr21:47948800-47970400	Strong transcription	Placenta	Placenta
14	chr21:47948800-47979400	Strong transcription	Liver	Liver
15	chr21:47949000-47969000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr21:47949000-47979000	Strong transcription	Adipose Nuclei	Adipose
17	chr21:47949000-47988200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr21:47949000-47993600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr21:47949600-47968600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr21:47949600-47970200	Strong transcription	Duodenum Mucosa	Duodenum
21	chr21:47949800-47967800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr21:47949800-47991800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr21:47950000-47968800	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr21:47950000-47989200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr21:47950000-47991000	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr21:47950200-47993200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr21:47950400-47971800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr21:47950400-47974400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr21:47952000-47978600	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr21:47952200-47968200	Strong transcription	Fetal Brain Female	brain
31	chr21:47953000-47974800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr21:47953000-47988200	Strong transcription	Gastric	stomach
33	chr21:47953000-47988600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr21:47953200-47968400	Strong transcription	Lung	lung
35	chr21:47953200-47968400	Strong transcription	Spleen	Spleen
36	chr21:47953200-47968600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr21:47953200-47968800	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr21:47953200-47971800	Strong transcription	Thymus	Thymus
39	chr21:47953200-47972000	Strong transcription	Ovary	ovary
40	chr21:47953200-47983400	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr21:47953200-47988400	Strong transcription	Fetal Intestine Small	intestine
42	chr21:47953200-47993000	Strong transcription	Osteobl	bone
43	chr21:47953400-47967600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr21:47953400-47969200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr21:47953400-47969200	Strong transcription	HSMMtube	muscle
46	chr21:47953400-47972000	Strong transcription	Brain Angular Gyrus	brain
47	chr21:47953400-47988000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr21:47953800-47968800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr21:47954200-47969200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr21:47954400-47973000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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