Variant report

Variant	rs2830931
Chromosome Location	chr21:28797967-28797968
allele	A/C
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	GATA3	chr21:28797569-28799176	SK-N-SH	brain:	n/a	chr21:28798474-28798495 chr21:28797729-28797738 chr21:28797726-28797742 chr21:28797731-28797738 chr21:28797724-28797745 chr21:28797731-28797738 chr21:28797731-28797738 chr21:28797807-28797823
2	PBX3	chr21:28797823-28798351	SK-N-SH	brain:	n/a	n/a
3	MAX	chr21:28797886-28798366	SK-N-SH	brain:	n/a	chr21:28798143-28798158 chr21:28798147-28798156 chr21:28798148-28798155 chr21:28798146-28798157 chr21:28798146-28798157
4	GATA2	chr21:28797939-28798253	SH-SY5Y	brain:	n/a	n/a
5	MXI1	chr21:28797550-28799237	SK-N-SH	brain:	n/a	n/a
6	EP300	chr21:28797839-28798224	SK-N-SH_RA	brain:	n/a	chr21:28797849-28797863 chr21:28798082-28798095
7	GATA3	chr21:28797802-28798508	SK-N-SH	brain:	n/a	chr21:28798474-28798495 chr21:28797807-28797823
8	CTCF	chr21:28797920-28798070	BE2_C	brain:	n/a	n/a
9	TCF12	chr21:28797858-28798471	SK-N-SH	brain:	n/a	chr21:28797930-28797938
10	TCF12	chr21:28797675-28798471	SK-N-SH	brain:	n/a	chr21:28797930-28797938
11	MAX	chr21:28797896-28798371	SK-N-SH	brain:	n/a	chr21:28798143-28798158 chr21:28798147-28798156 chr21:28798148-28798155 chr21:28798146-28798157 chr21:28798146-28798157
12	PBX3	chr21:28797833-28798362	SK-N-SH	brain:	n/a	n/a
13	EP300	chr21:28797803-28798184	SK-N-SH_RA	brain:	n/a	chr21:28797849-28797863 chr21:28797816-28797825 chr21:28798082-28798095

Variant related genes	Relation type
RPL10P1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16980566	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16980576	1.00[AFR][1000 genomes]
rs16980647	0.93[JPT][hapmap];0.88[AMR][1000 genomes]
rs183006	0.82[EUR][1000 genomes]
rs1979179	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs239659	0.82[EUR][1000 genomes]
rs239661	0.82[EUR][1000 genomes]
rs239662	0.82[EUR][1000 genomes]
rs239663	0.83[EUR][1000 genomes]
rs239664	0.82[EUR][1000 genomes]
rs239666	0.82[EUR][1000 genomes]
rs239678	0.82[EUR][1000 genomes]
rs2409206	0.89[CEU][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2830928	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2830930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830932	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830934	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830936	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2830937	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2830938	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56865146	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57333997	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59472353	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72635039	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72635040	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72635041	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72635042	0.94[AMR][1000 genomes];1.00[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	nsv916307	chr21:28762455-28905095	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28789200-28798000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:28789400-28798000	Weak transcription	Spleen	Spleen
3	chr21:28789400-28802000	Weak transcription	Left Ventricle	heart
4	chr21:28793000-28798800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr21:28793200-28798000	Weak transcription	Pancreas	Pancrea
6	chr21:28793800-28798600	Enhancers	Osteobl	bone
7	chr21:28793800-28798800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr21:28793800-28799000	Enhancers	NHDF-Ad	bronchial
9	chr21:28794000-28798000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr21:28794000-28798200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr21:28794000-28798600	Enhancers	Adipose Nuclei	Adipose
12	chr21:28794000-28798600	Enhancers	NHLF	lung
13	chr21:28794000-28799200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr21:28794200-28798800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr21:28794200-28799000	Enhancers	HSMM	muscle
16	chr21:28794600-28798600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr21:28794600-28798800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr21:28794600-28798800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr21:28794600-28798800	Enhancers	HMEC	breast
20	chr21:28795200-28798400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr21:28795400-28798000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr21:28795400-28798400	Enhancers	Placenta	Placenta
23	chr21:28795400-28798400	Enhancers	NHEK	skin
24	chr21:28795600-28798000	Weak transcription	Fetal Muscle Leg	muscle
25	chr21:28795600-28798000	Weak transcription	Psoas Muscle	Psoas
26	chr21:28795600-28798000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr21:28795600-28801800	Weak transcription	Aorta	Aorta
28	chr21:28796000-28798200	Enhancers	Fetal Intestine Small	intestine
29	chr21:28796400-28798400	Enhancers	Ovary	ovary
30	chr21:28796600-28801800	Weak transcription	Fetal Stomach	stomach
31	chr21:28796800-28798400	Enhancers	Dnd41	blood
32	chr21:28796800-28798800	Enhancers	HSMMtube	muscle
33	chr21:28797000-28798000	Weak transcription	Right Ventricle	heart
34	chr21:28797000-28798000	Weak transcription	NH-A	brain
35	chr21:28797000-28798200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr21:28797200-28798000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr21:28797200-28798000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr21:28797200-28798400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr21:28797800-28798200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr21:28797800-28798200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr21:28797800-28798200	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr21:28797800-28798200	Enhancers	Stomach Smooth Muscle	stomach
43	chr21:28797800-28798400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr21:28797800-28798400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr21:28797800-28801800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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