Variant report

Variant	rs580007
Chromosome Location	chr21:44779138-44779139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44778568..44780302-chr21:44848836..44851138,2	MCF-7	breast:
2	chr21:44773099..44775233-chr21:44777040..44779617,2	MCF-7	breast:
3	chr21:44778477..44780291-chr21:44788253..44791187,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIK1-5	chr21:44777715-44779366	XLOC_014102
2	lnc-SIK1-5	chr21:44777430-44779366	XLOC_014102

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2073428	0.87[EUR][1000 genomes]
rs478075	0.84[EUR][1000 genomes]
rs535024	0.85[EUR][1000 genomes]
rs564779	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs565629	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs587329	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs622330	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs666699	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs672929	0.84[EUR][1000 genomes]
rs7280794	0.87[EUR][1000 genomes]
rs857566	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs857567	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv1817359	chr21:44699077-44821595	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1059062	chr21:44711272-44779969	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1057726	chr21:44711850-44957303	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
6	nsv544466	chr21:44711850-44957303	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
7	nsv1058308	chr21:44722915-44825108	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1063186	chr21:44729904-44828476	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv544467	chr21:44729904-44828476	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv913837	chr21:44731138-44853859	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
11	nsv913838	chr21:44740134-44931821	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
12	nsv913839	chr21:44750200-44931821	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
13	nsv913840	chr21:44750643-44823479	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv913841	chr21:44761874-44853859	Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
15	nsv913842	chr21:44764895-44792929	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv913843	chr21:44774757-44810756	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44754800-44781200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:44763600-44780800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr21:44768400-44781000	Weak transcription	Fetal Intestine Small	intestine
4	chr21:44769000-44780600	Weak transcription	Right Atrium	heart
5	chr21:44770200-44780400	Weak transcription	Esophagus	oesophagus
6	chr21:44772400-44780800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr21:44772400-44781200	Enhancers	Fetal Muscle Leg	muscle
8	chr21:44774000-44780200	Weak transcription	Spleen	Spleen
9	chr21:44774200-44779400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr21:44774600-44780600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr21:44774800-44782000	Weak transcription	Brain Anterior Caudate	brain
12	chr21:44775600-44779200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr21:44776600-44780600	Weak transcription	Fetal Heart	heart
14	chr21:44776600-44780800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:44776600-44780800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr21:44776600-44781000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr21:44776600-44781000	Weak transcription	Fetal Brain Female	brain
18	chr21:44777200-44780000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr21:44777200-44782000	Enhancers	Brain Germinal Matrix	brain
20	chr21:44777400-44788600	Enhancers	Fetal Brain Male	brain
21	chr21:44777600-44779800	Enhancers	Brain Hippocampus Middle	brain
22	chr21:44778000-44781000	Enhancers	GM12878-XiMat	blood
23	chr21:44778200-44780200	Enhancers	Fetal Lung	lung
24	chr21:44778200-44781200	Enhancers	Primary B cells from peripheral blood	blood
25	chr21:44778600-44779200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr21:44778600-44779400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
27	chr21:44778600-44781000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
28	chr21:44778800-44779200	Enhancers	Psoas Muscle	Psoas
29	chr21:44778800-44779400	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr21:44778800-44779600	Enhancers	Brain Cingulate Gyrus	brain
31	chr21:44778800-44781400	Enhancers	Fetal Thymus	thymus
32	chr21:44779000-44779200	Enhancers	Brain Angular Gyrus	brain
33	chr21:44779000-44779600	Enhancers	Gastric	stomach
34	chr21:44779000-44780000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
35	chr21:44779000-44780400	Weak transcription	Lung	lung
36	chr21:44779000-44781600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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