Variant report

Variant	rs2839060
Chromosome Location	chr21:47342116-47342117
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:47300090..47300627-chr21:47342032..47342538,2	MCF-7	breast:
2	chr21:47328644..47331016-chr21:47340908..47343121,3	MCF-7	breast:
3	chr21:47267610..47268453-chr21:47342093..47343648,5	MCF-7	breast:
4	chr21:47336465..47338261-chr21:47339874..47342406,2	K562	blood:
5	chr21:47329285..47331470-chr21:47342066..47344987,2	MCF-7	breast:
6	chr21:47286434..47288542-chr21:47340592..47343360,3	MCF-7	breast:
7	chr21:47338168..47340965-chr21:47341072..47342617,2	K562	blood:
8	chr21:47338875..47340965-chr21:47341117..47343595,2	K562	blood:
9	chr21:47300119..47302715-chr21:47341992..47344397,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1547240	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs1736419	0.97[ASN][1000 genomes]
rs1736420	0.95[CHB][hapmap]
rs1783075	0.95[CHB][hapmap]
rs2070437	0.95[CHB][hapmap]
rs2075908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs2075909	0.93[EUR][1000 genomes]
rs2839042	0.84[CHB][hapmap]
rs2839043	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2839044	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs2839045	0.83[CHB][hapmap]
rs2839046	0.84[CHB][hapmap]
rs2839048	0.84[CHB][hapmap]
rs2839052	0.84[CHB][hapmap]
rs373617	0.95[CHB][hapmap]
rs381083	0.95[CHB][hapmap]
rs395418	0.97[ASN][1000 genomes]
rs431609	0.95[CHB][hapmap]
rs437264	0.94[CHB][hapmap]
rs440207	0.93[EUR][1000 genomes]
rs452332	0.95[CHB][hapmap]
rs4819162	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs4819164	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs4819168	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs4819169	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819174	0.95[ASN][1000 genomes]
rs7277160	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7281469	0.83[CHB][hapmap]
rs7283763	0.83[CHB][hapmap]
rs8132054	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs8133743	0.89[CHB][hapmap]
rs8133858	0.84[CHD][hapmap]
rs9306144	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9975216	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9980566	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2839060	SIK1	cis	parietal	SCAN
rs2839060	KRTAP12-2	cis	cerebellum	SCAN
rs2839060	COL6A1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47308000-47343000	Weak transcription	Right Atrium	heart
2	chr21:47330800-47342200	Weak transcription	Brain Hippocampus Middle	brain
3	chr21:47333600-47351600	Weak transcription	Gastric	stomach
4	chr21:47336800-47342600	Weak transcription	Fetal Thymus	thymus
5	chr21:47339600-47343600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr21:47339800-47343000	Weak transcription	Spleen	Spleen
7	chr21:47340000-47354800	Weak transcription	Primary T cells from cord blood	blood
8	chr21:47340200-47342600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr21:47340600-47342200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr21:47340800-47342600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr21:47340800-47342800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr21:47340800-47343000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr21:47341000-47342600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr21:47341800-47342200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr21:47341800-47342800	Enhancers	NHLF	lung
16	chr21:47341800-47343200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr21:47341800-47343600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr21:47341800-47343600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr21:47341800-47343600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr21:47341800-47343600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr21:47341800-47343600	Enhancers	Fetal Muscle Leg	muscle

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