Variant report

Variant	rs9978439
Chromosome Location	chr21:47343022-47343023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47240324..47241096-chr21:47342788..47343697,3	MCF-7	breast:
2	chr21:47240289..47241171-chr21:47342639..47343656,4	MCF-7	breast:
3	chr21:47188474..47189148-chr21:47343010..47343629,2	MCF-7	breast:
4	chr21:46976073..46976581-chr21:47342782..47343760,2	MCF-7	breast:
5	chr21:47300028..47300909-chr21:47342650..47343811,5	MCF-7	breast:
6	chr21:47328644..47331016-chr21:47340908..47343121,3	MCF-7	breast:
7	chr21:47267694..47268408-chr21:47342147..47343416,5	MCF-7	breast:
8	chr21:47267610..47268453-chr21:47342093..47343648,5	MCF-7	breast:
9	chr21:47329285..47331470-chr21:47342066..47344987,2	MCF-7	breast:
10	chr21:47286434..47288542-chr21:47340592..47343360,3	MCF-7	breast:
11	chr21:47242790..47243479-chr21:47342941..47343666,2	MCF-7	breast:
12	chr21:47299971..47300594-chr21:47342907..47343695,3	MCF-7	breast:
13	chr21:47338875..47340965-chr21:47341117..47343595,2	K562	blood:
14	chr21:47300119..47302715-chr21:47341992..47344397,3	MCF-7	breast:
15	chr21:47342692..47343850-chr21:47390349..47391235,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13050871	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13052792	0.82[EUR][1000 genomes]
rs1736421	0.91[ASN][1000 genomes]
rs1980979	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839070	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34101341	0.86[EUR][1000 genomes]
rs34898755	0.82[EUR][1000 genomes]
rs35564189	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs368033	0.91[ASN][1000 genomes]
rs372748	0.91[ASN][1000 genomes]
rs3788237	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788240	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3827268	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384068	0.91[ASN][1000 genomes]
rs387320	0.91[ASN][1000 genomes]
rs399595	0.91[ASN][1000 genomes]
rs401411	0.91[ASN][1000 genomes]
rs411390	0.91[ASN][1000 genomes]
rs431162	0.91[ASN][1000 genomes]
rs439334	0.86[ASN][1000 genomes]
rs71324470	0.90[EUR][1000 genomes]
rs7277508	0.80[EUR][1000 genomes]
rs73907994	1.00[ASN][1000 genomes]
rs8131266	1.00[ASN][1000 genomes]
rs9979027	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
4	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
6	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
8	nsv428043	chr21:47179244-47471971	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a
9	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
10	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
11	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
12	nsv914083	chr21:47265786-47453954	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
13	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
14	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
15	nsv1062420	chr21:47311566-47347666	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
16	nsv1062386	chr21:47314890-47343364	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
17	nsv1061940	chr21:47317456-47343364	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
18	nsv1063852	chr21:47317456-47358709	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
19	nsv1060235	chr21:47317456-47360544	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
20	nsv587866	chr21:47338608-47345060	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
21	nsv587867	chr21:47338723-47344584	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
22	nsv587868	chr21:47342116-47344584	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
23	nsv587869	chr21:47342116-47345060	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
24	nsv914085	chr21:47342116-47433055	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
25	esv3363667	chr21:47342524-47346122	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
26	esv3336989	chr21:47342624-47346122	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47333600-47351600	Weak transcription	Gastric	stomach
2	chr21:47339600-47343600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr21:47340000-47354800	Weak transcription	Primary T cells from cord blood	blood
4	chr21:47341800-47343200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
5	chr21:47341800-47343600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr21:47341800-47343600	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr21:47341800-47343600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr21:47341800-47343600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr21:47341800-47343600	Enhancers	Fetal Muscle Leg	muscle
10	chr21:47342200-47343600	Enhancers	Brain Hippocampus Middle	brain
11	chr21:47342400-47343600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr21:47342400-47343600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr21:47342400-47343600	Enhancers	Brain Cingulate Gyrus	brain
14	chr21:47342600-47343200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr21:47342600-47343200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr21:47342600-47343200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr21:47342600-47343200	Enhancers	Brain Anterior Caudate	brain
18	chr21:47342600-47343200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr21:47342600-47343200	ZNF genes & repeats	Fetal Thymus	thymus
20	chr21:47342600-47343200	Enhancers	NHDF-Ad	bronchial
21	chr21:47342600-47343600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr21:47342600-47343600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr21:47342600-47343600	Enhancers	HSMM	muscle
24	chr21:47342600-47343800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr21:47342600-47344200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr21:47342800-47343200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr21:47342800-47343200	Enhancers	Fetal Kidney	kidney
28	chr21:47342800-47343200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
29	chr21:47342800-47343400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr21:47342800-47343400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr21:47342800-47343600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr21:47342800-47343600	Enhancers	Brain Angular Gyrus	brain
33	chr21:47342800-47343600	Enhancers	Brain Substantia Nigra	brain
34	chr21:47343000-47343200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr21:47343000-47343200	Enhancers	Fetal Lung	lung
36	chr21:47343000-47343200	Enhancers	Right Atrium	heart
37	chr21:47343000-47343200	Enhancers	Spleen	Spleen
38	chr21:47343000-47343600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr21:47343000-47343600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr21:47343000-47343600	Enhancers	Adipose Nuclei	Adipose
41	chr21:47343000-47343600	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr21:47343000-47343600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr21:47343000-47343600	Enhancers	Fetal Heart	heart
44	chr21:47343000-47343600	Enhancers	Placenta	Placenta
45	chr21:47343000-47343600	Enhancers	Fetal Stomach	stomach
46	chr21:47343000-47343600	Enhancers	Left Ventricle	heart
47	chr21:47343000-47343600	Enhancers	Rectal Smooth Muscle	rectum

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