Variant report

Variant	rs1452094
Chromosome Location	chr21:28744290-28744291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr21:28744283-28744775	SK-N-SH	brain:	n/a	n/a
2	REST	chr21:28744099-28744620	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr21:28744101-28744676	H1-neurons	neurons:	n/a	n/a
4	TCF12	chr21:28743972-28744846	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr21:28743585-28745082	SK-N-SH	brain:	n/a	chr21:28743806-28743813 chr21:28744411-28744421 chr21:28743650-28743671 chr21:28744350-28744360 chr21:28744100-28744121 chr21:28744408-28744424 chr21:28743806-28743813 chr21:28743799-28743820 chr21:28744483-28744492 chr21:28743804-28743813 chr21:28743806-28743813 chr21:28744483-28744490 chr21:28744107-28744116
6	POLR2A	chr21:28744119-28744589	H1-neurons	neurons:	n/a	n/a
7	GATA3	chr21:28743847-28745083	SK-N-SH	brain:	n/a	chr21:28744411-28744421 chr21:28744350-28744360 chr21:28744100-28744121 chr21:28744408-28744424 chr21:28744483-28744492 chr21:28744483-28744490 chr21:28744107-28744116
8	GATA2	chr21:28744240-28744639	HUVEC	blood vessel:	n/a	chr21:28744411-28744421 chr21:28744407-28744421 chr21:28744350-28744360 chr21:28744408-28744424 chr21:28744483-28744492 chr21:28744483-28744490
9	EP300	chr21:28744091-28744647	Hela-S3	cervix:	n/a	chr21:28744526-28744540

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:28743113..28745036-chr21:28748011..28750615,2	K562	blood:

Variant related genes	Relation type
EIF4A1P1	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1023381	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1023382	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1023383	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1155213	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1155214	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11702075	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11702106	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11702121	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13052258	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1349598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1376927	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1452093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][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]
rs1452095	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1452096	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1452097	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1452098	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1452099	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1452100	0.82[ASN][1000 genomes]
rs1452101	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1557366	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1571670	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1597786	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1597787	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1597788	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1597789	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16997563	0.81[YRI][hapmap]
rs16997565	0.81[YRI][hapmap]
rs1817113	0.80[AMR][1000 genomes]
rs1817114	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1869147	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1893579	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1893580	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1893581	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2016760	0.82[AMR][1000 genomes]
rs2016768	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2123151	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2123152	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167597	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2218932	0.82[ASN][1000 genomes]
rs2409205	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2830860	0.82[ASN][1000 genomes]
rs2830869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2830871	1.00[CEU][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2830872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2830873	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2830874	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2830875	0.84[ASN][1000 genomes]
rs2830876	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2830877	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2830878	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2830879	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2830880	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2830881	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2830882	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2830883	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2830884	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830885	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2830886	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2830887	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2830888	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2830891	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2830893	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830894	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830895	0.99[ASN][1000 genomes]
rs28555164	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28692542	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2898109	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2898111	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34495779	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4589839	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4589840	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62222042	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6516763	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs751950	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs751951	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs754017	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8134899	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs986975	0.82[ASN][1000 genomes]
rs995532	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs995533	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9975646	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9976078	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9976291	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9976514	0.82[ASN][1000 genomes]
rs9977499	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9978629	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9978787	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9979152	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9980089	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9982621	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv459229	chr21:28543456-29482488	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv587342	chr21:28543456-29482488	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv913666	chr21:28687650-28810976	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1061112	chr21:28738028-28775601	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1452094	NCRNA00258	cis	parietal	SCAN
rs1452094	NCRNA00258	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28741200-28745600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr21:28741400-28744800	Enhancers	Dnd41	blood
3	chr21:28741600-28744400	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr21:28741800-28745200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr21:28742200-28744400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr21:28742200-28763600	Weak transcription	Left Ventricle	heart
7	chr21:28742400-28745200	Enhancers	Fetal Heart	heart
8	chr21:28742400-28745800	Enhancers	Fetal Lung	lung
9	chr21:28742600-28745600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr21:28742600-28745600	Enhancers	HSMMtube	muscle
11	chr21:28742800-28745600	Enhancers	HSMM	muscle
12	chr21:28743200-28744400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr21:28743200-28744400	Weak transcription	Right Atrium	heart
14	chr21:28743200-28745200	Weak transcription	Placenta	Placenta
15	chr21:28743200-28745200	Weak transcription	Ovary	ovary
16	chr21:28743400-28744400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr21:28743400-28744600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr21:28743400-28745200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr21:28743400-28745400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr21:28743600-28744400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr21:28743600-28744400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr21:28743600-28745000	Enhancers	Osteobl	bone
23	chr21:28743600-28745200	Weak transcription	Fetal Stomach	stomach
24	chr21:28743800-28744600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr21:28743800-28744600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr21:28744000-28745400	Enhancers	NH-A	brain
27	chr21:28744200-28744600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr21:28744200-28744800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr21:28744200-28744800	Enhancers	NHLF	lung

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