Variant report

Variant	rs2839039
Chromosome Location	chr21:47321499-47321500
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47311846..47315136-chr21:47319001..47321928,3	K562	blood:

Variant related genes	Relation type
ENSG00000183570	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1059010	1.00[ASN][1000 genomes]
rs10854474	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10854475	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089025	1.00[ASN][1000 genomes]
rs1124309	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11701693	1.00[ASN][1000 genomes]
rs1625244	1.00[ASN][1000 genomes]
rs1736424	1.00[ASN][1000 genomes]
rs1783076	1.00[ASN][1000 genomes]
rs2014421	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2026286	1.00[ASN][1000 genomes]
rs2150453	0.86[ASW][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2150454	1.00[ASN][1000 genomes]
rs2183599	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2210290	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277812	1.00[ASN][1000 genomes]
rs2330327	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2776402	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs2839020	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs2839021	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs2839030	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2839033	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs2839035	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2839041	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839050	0.87[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839054	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34495634	1.00[ASN][1000 genomes]
rs34686582	1.00[CHB][hapmap]
rs34990419	1.00[ASN][1000 genomes]
rs369245	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371587	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373267	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374331	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375254	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375971	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377213	1.00[ASN][1000 genomes]
rs3788217	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs3788218	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3788226	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs3788228	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs380120	1.00[ASN][1000 genomes]
rs382195	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs382303	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402039	0.85[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs402355	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403192	1.00[ASN][1000 genomes]
rs407651	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410902	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413246	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413517	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420386	1.00[ASN][1000 genomes]
rs425232	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs432338	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4369958	1.00[ASN][1000 genomes]
rs439145	1.00[ASN][1000 genomes]
rs442953	1.00[ASN][1000 genomes]
rs451920	1.00[ASN][1000 genomes]
rs452797	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454268	1.00[ASN][1000 genomes]
rs4818804	1.00[ASN][1000 genomes]
rs4819143	1.00[ASN][1000 genomes]
rs4819159	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs56695931	1.00[ASN][1000 genomes]
rs6518257	1.00[ASN][1000 genomes]
rs6518258	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6518259	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324446	1.00[ASN][1000 genomes]
rs7276114	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs7277632	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279887	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7280054	1.00[ASN][1000 genomes]
rs7280405	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7283688	1.00[ASN][1000 genomes]
rs73159604	1.00[ASN][1000 genomes]
rs7410101	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7410105	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs753092	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs760436	0.90[GIH][hapmap]
rs8131193	1.00[CHB][hapmap]
rs8133932	1.00[ASN][1000 genomes]
rs9637207	1.00[ASN][1000 genomes]
rs9653780	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs9653791	0.90[CEU][hapmap];1.00[ASN][1000 genomes]
rs989650	1.00[ASN][1000 genomes]
rs9976042	1.00[ASN][1000 genomes]
rs9980645	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv914082	chr21:47265786-47338007	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
13	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
14	nsv914084	chr21:47288453-47326666	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
15	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
16	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
17	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
18	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
19	nsv587865	chr21:47317069-47331964	Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
20	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
21	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
22	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2839039	FTCD	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47308000-47343000	Weak transcription	Right Atrium	heart
2	chr21:47313200-47335600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr21:47313800-47321600	Weak transcription	Primary T cells from cord blood	blood
4	chr21:47314400-47330200	Weak transcription	Brain Hippocampus Middle	brain
5	chr21:47314600-47324600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr21:47314600-47327400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr21:47314600-47330200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr21:47315000-47330200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr21:47315200-47323400	Weak transcription	HSMMtube	muscle
10	chr21:47315200-47330200	Weak transcription	Adipose Nuclei	Adipose
11	chr21:47316200-47322600	Weak transcription	Fetal Thymus	thymus
12	chr21:47316200-47326600	Strong transcription	Thymus	Thymus
13	chr21:47317600-47322400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr21:47317800-47322400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr21:47320200-47330200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr21:47320800-47321600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr21:47320800-47326000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr21:47321000-47321800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr21:47321000-47323200	Strong transcription	Spleen	Spleen
20	chr21:47321200-47326000	Weak transcription	Fetal Stomach	stomach
21	chr21:47321400-47321600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr21:47321400-47321800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
23	chr21:47321400-47321800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast

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