Variant report

Variant	rs13050554
Chromosome Location	chr21:45579901-45579902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:45551834..45580791-chr21:45711953..45732193,97	MCF-7	breast:
2	chr21:45577492..45580364-chr21:45620942..45622616,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ICOSLG-6	chr21:45579708-45579955	XLOC_014110
2	lnc-ICOSLG-6	chr21:45578913-45580684	XLOC_014110
3	lnc-ICOSLG-6	chr21:45579708-45579959	XLOC_014110

Variant related genes	Relation type
ENSG00000232124	Chromatin interaction
ENSG00000141959	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2838505	0.85[EUR][1000 genomes]
rs2838506	0.85[EUR][1000 genomes]
rs7283041	0.91[AMR][1000 genomes]
rs9982806	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv913890	chr21:45482950-45603746	Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv459294	chr21:45499171-45595060	Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv587722	chr21:45499171-45595060	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv913891	chr21:45508561-45588518	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv913892	chr21:45508561-45595060	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv913893	chr21:45508561-45603746	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv913894	chr21:45508561-45627976	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv913895	chr21:45528919-45595060	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv913896	chr21:45528919-45603746	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
15	nsv913897	chr21:45528919-45640139	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
17	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
18	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
19	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	74 gene(s)	inside rSNPs	diseases
20	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
21	nsv1065479	chr21:45571324-45617878	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv913899	chr21:45577102-45611950	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	nsv913900	chr21:45577102-45640139	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45561000-45584400	Weak transcription	Aorta	Aorta
2	chr21:45565400-45580600	Weak transcription	Brain Germinal Matrix	brain
3	chr21:45571000-45582600	Weak transcription	Ovary	ovary
4	chr21:45573600-45580000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr21:45573800-45580400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr21:45575400-45580200	Weak transcription	NHLF	lung
7	chr21:45575400-45580400	Weak transcription	NHDF-Ad	bronchial
8	chr21:45575400-45583400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr21:45575400-45586000	Weak transcription	Fetal Lung	lung
10	chr21:45575400-45592000	Weak transcription	Fetal Brain Female	brain
11	chr21:45575600-45584800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr21:45576000-45580400	Weak transcription	Psoas Muscle	Psoas
13	chr21:45576000-45580600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr21:45576600-45580200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr21:45576600-45580600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr21:45576600-45580600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr21:45576600-45581200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr21:45576800-45580000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr21:45576800-45580400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr21:45576800-45580600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr21:45577000-45580200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr21:45577200-45580600	Enhancers	Fetal Muscle Trunk	muscle
23	chr21:45577200-45581000	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr21:45577600-45581400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr21:45578600-45580200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr21:45578600-45580200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr21:45578600-45580400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr21:45578600-45580600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr21:45578800-45580200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr21:45578800-45580200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr21:45578800-45580200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr21:45578800-45580200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr21:45578800-45580400	Flanking Active TSS	Thymus	Thymus
34	chr21:45578800-45581400	Flanking Active TSS	GM12878-XiMat	blood
35	chr21:45579000-45580000	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr21:45579000-45580000	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr21:45579000-45580200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr21:45579000-45580200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr21:45579000-45580200	Enhancers	Brain Substantia Nigra	brain
40	chr21:45579000-45580200	Flanking Active TSS	Fetal Thymus	thymus
41	chr21:45579000-45580200	Active TSS	Rectal Smooth Muscle	rectum
42	chr21:45579000-45580400	Enhancers	HSMMtube	muscle
43	chr21:45579000-45580800	Enhancers	HUVEC	blood vessel
44	chr21:45579000-45581000	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr21:45579000-45581200	Enhancers	Lung	lung
46	chr21:45579200-45580000	Enhancers	Fetal Heart	heart
47	chr21:45579200-45580200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr21:45579200-45580200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr21:45579200-45580800	Enhancers	Fetal Intestine Small	intestine
50	chr21:45579200-45580800	Enhancers	Stomach Mucosa	stomach

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