Variant report

Variant	rs9976485
Chromosome Location	chr21:44897485-44897486
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44844513..44847028-chr21:44896090..44898476,3	MCF-7	breast:
2	chr21:44889384..44891678-chr21:44897069..44899514,2	MCF-7	breast:
3	chr21:44845300..44847878-chr21:44896244..44899559,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIK1-4	chr21:44896862-44898009	NONHSAT082414

Variant related genes	Relation type
ENSG00000185186	Chromatin interaction
ENSG00000142178	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17004561	0.85[AFR][1000 genomes]
rs17004562	0.85[AFR][1000 genomes]
rs17004563	1.00[AFR][1000 genomes]
rs17004567	0.85[AFR][1000 genomes]
rs17004568	0.85[AFR][1000 genomes]
rs17004569	0.91[AFR][1000 genomes]
rs28548333	0.91[AFR][1000 genomes]
rs28569783	0.85[AFR][1000 genomes]
rs28796434	0.85[AFR][1000 genomes]
rs8133655	0.85[AFR][1000 genomes]
rs9980031	1.00[AFR][1000 genomes]
rs9980407	0.91[AFR][1000 genomes]
rs9981510	1.00[AFR][1000 genomes]
rs9983070	1.00[AFR][1000 genomes]
rs9984553	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv913847	chr21:44792003-44931821	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
7	nsv913849	chr21:44817248-44925334	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	nsv913852	chr21:44829087-44925334	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
9	nsv913860	chr21:44831981-44925334	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS 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	95 gene(s)	inside rSNPs	diseases
10	nsv913867	chr21:44835508-44925334	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv913868	chr21:44835508-44954522	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	98 gene(s)	inside rSNPs	diseases
12	nsv913872	chr21:44860542-44925334	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	esv1839560	chr21:44864079-44973184	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
14	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
15	nsv587689	chr21:44884252-44986050	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
16	nsv1061369	chr21:44886596-44931388	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv544468	chr21:44886596-44931388	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	nsv1059264	chr21:44895863-44944515	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44892400-44902200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr21:44892600-44901600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr21:44894600-44897600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr21:44894600-44897600	Weak transcription	HSMM	muscle
5	chr21:44894600-44905400	Weak transcription	HSMMtube	muscle
6	chr21:44896200-44898600	Flanking Active TSS	Hela-S3	cervix
7	chr21:44896200-44899600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr21:44896200-44900600	Enhancers	Fetal Muscle Leg	muscle
9	chr21:44896200-44900600	Enhancers	Right Ventricle	heart
10	chr21:44896200-44901400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr21:44896400-44899600	Enhancers	Fetal Stomach	stomach
12	chr21:44896400-44899800	Enhancers	Placenta	Placenta
13	chr21:44896400-44901200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr21:44896600-44897600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:44896600-44897800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr21:44896600-44898800	Enhancers	Pancreas	Pancrea
17	chr21:44896600-44899000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr21:44896800-44897600	Enhancers	Colon Smooth Muscle	Colon
19	chr21:44896800-44899000	Enhancers	Fetal Intestine Large	intestine
20	chr21:44897000-44897600	Enhancers	Liver	Liver
21	chr21:44897000-44898600	Flanking Active TSS	A549	lung
22	chr21:44897000-44898800	Enhancers	Fetal Intestine Small	intestine
23	chr21:44897000-44899000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr21:44897000-44899400	Enhancers	Stomach Mucosa	stomach
25	chr21:44897000-44900400	Enhancers	Left Ventricle	heart
26	chr21:44897200-44897600	Enhancers	Stomach Smooth Muscle	stomach
27	chr21:44897200-44897600	Enhancers	NHEK	skin
28	chr21:44897200-44897800	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr21:44897200-44897800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr21:44897200-44897800	Flanking Active TSS	HepG2	liver
31	chr21:44897200-44898200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr21:44897200-44898600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr21:44897200-44898600	Enhancers	Fetal Thymus	thymus
34	chr21:44897200-44898600	Enhancers	Spleen	Spleen
35	chr21:44897200-44898800	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr21:44897200-44898800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr21:44897200-44899000	Enhancers	Duodenum Mucosa	Duodenum
38	chr21:44897200-44899000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr21:44897200-44899200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr21:44897200-44899200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr21:44897200-44899400	Enhancers	NH-A	brain
42	chr21:44897200-44900200	Enhancers	HUVEC	blood vessel
43	chr21:44897200-44900400	Enhancers	Lung	lung
44	chr21:44897400-44897600	Enhancers	Adipose Nuclei	Adipose
45	chr21:44897400-44897600	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr21:44897400-44897800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr21:44897400-44897800	Enhancers	Brain Substantia Nigra	brain
48	chr21:44897400-44897800	Flanking Active TSS	HMEC	breast
49	chr21:44897400-44898400	Enhancers	Osteobl	bone
50	chr21:44897400-44898600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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