Variant report

Variant	rs28971677
Chromosome Location	chr21:44600220-44600221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44595907..44598227-chr21:44599190..44600855,2	MCF-7	breast:
2	chr21:44595975..44600241-chr21:44843202..44849395,11	MCF-7	breast:
3	chr21:44596302..44600320-chr21:44763162..44765941,4	MCF-7	breast:
4	chr21:44590676..44595436-chr21:44598084..44601687,4	K562	blood:
5	chr21:44599423..44602035-chr21:44607332..44609772,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1041453	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11203177	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11702241	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11909053	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11909888	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11910132	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11910213	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13048578	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2839640	0.93[EUR][1000 genomes]
rs2839641	0.80[ASN][1000 genomes]
rs2839642	0.82[ASN][1000 genomes]
rs2839643	0.82[ASN][1000 genomes]
rs2839647	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2839648	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28970980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919966	1.00[ASN][1000 genomes]
rs4919967	0.80[ASN][1000 genomes]
rs7276182	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7276342	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7280964	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913812	chr21:44213057-44686358	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1067412	chr21:44526656-44772130	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv1056684	chr21:44539714-44886119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1060276	chr21:44550394-44628579	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
6	nsv913832	chr21:44579105-44768562	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv3427846	chr21:44597783-44602181	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	esv3430571	chr21:44598283-44602181	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv3369197	chr21:44598383-44602181	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv3435307	chr21:44600215-44600741	Weak transcription Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44593800-44601600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:44595600-44602400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr21:44596400-44600400	Enhancers	Spleen	Spleen
4	chr21:44596600-44600800	Enhancers	Pancreas	Pancrea
5	chr21:44596600-44601600	Enhancers	HMEC	breast
6	chr21:44596800-44602400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr21:44597000-44601800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:44597200-44601400	Enhancers	Brain Germinal Matrix	brain
9	chr21:44597600-44601400	Enhancers	Fetal Brain Female	brain
10	chr21:44597600-44601600	Enhancers	Esophagus	oesophagus
11	chr21:44597800-44601400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr21:44598000-44600600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr21:44598000-44600800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr21:44598200-44600400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr21:44598200-44600400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr21:44598200-44600400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr21:44598200-44600400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr21:44598200-44601000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr21:44598200-44601600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr21:44598400-44600800	Enhancers	Fetal Heart	heart
21	chr21:44598400-44602800	Weak transcription	Brain Hippocampus Middle	brain
22	chr21:44598800-44601600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr21:44599000-44601200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr21:44599200-44603000	Weak transcription	Colonic Mucosa	Colon
25	chr21:44599200-44614200	Weak transcription	Right Atrium	heart
26	chr21:44599400-44601200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr21:44599800-44600600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr21:44599800-44601000	Weak transcription	Placenta	Placenta
29	chr21:44600000-44605800	Weak transcription	Gastric	stomach
30	chr21:44600200-44600600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr21:44600200-44600600	Bivalent Enhancer	Fetal Brain Male	brain
32	chr21:44600200-44600600	Enhancers	Fetal Lung	lung
33	chr21:44600200-44600600	Weak transcription	NHEK	skin
34	chr21:44600200-44611200	Weak transcription	Primary T cells from cord blood	blood

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