Variant report

Variant	rs2838311
Chromosome Location	chr21:44891160-44891161
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44891072..44892849-chr21:44897824..44900238,2	MCF-7	breast:
2	chr21:44889384..44891678-chr21:44897069..44899514,2	MCF-7	breast:
3	chr21:44868612..44870635-chr21:44890162..44893361,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIK1-4	chr21:44890958-44891198	XLOC_014105
2	lnc-SIK1-4	chr21:44890958-44891198	XLOC_014105
3	lnc-SIK1-4	chr21:44890876-44891198	XLOC_014105

Variant related genes	Relation type
ENSG00000188660	Chromatin interaction
ENSG00000185186	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs162379	0.82[YRI][hapmap]
rs2838334	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44882600-44891200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr21:44885600-44894000	Weak transcription	Hela-S3	cervix
3	chr21:44887600-44891600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr21:44888000-44891800	Enhancers	Fetal Intestine Large	intestine
5	chr21:44888000-44894000	Weak transcription	A549	lung
6	chr21:44888000-44897200	Weak transcription	HUVEC	blood vessel
7	chr21:44888200-44892600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr21:44888400-44891200	Weak transcription	Right Atrium	heart
9	chr21:44888400-44892000	Weak transcription	Fetal Kidney	kidney
10	chr21:44888600-44891400	Weak transcription	Fetal Lung	lung
11	chr21:44888600-44891400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr21:44888800-44891200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr21:44889000-44891200	Enhancers	Esophagus	oesophagus
14	chr21:44889000-44891400	Enhancers	Fetal Muscle Leg	muscle
15	chr21:44889000-44897000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr21:44890000-44891400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr21:44890000-44891400	Weak transcription	Placenta	Placenta
18	chr21:44890000-44891600	Weak transcription	NH-A	brain
19	chr21:44890000-44893000	Weak transcription	HSMM	muscle
20	chr21:44890000-44896600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr21:44890200-44891200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr21:44890200-44897000	Weak transcription	Stomach Mucosa	stomach
23	chr21:44890200-44897200	Weak transcription	Spleen	Spleen
24	chr21:44890200-44897200	Weak transcription	NHEK	skin
25	chr21:44890400-44891400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr21:44890400-44892400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr21:44890400-44892400	Strong transcription	HSMMtube	muscle
28	chr21:44890400-44892600	Enhancers	Lung	lung
29	chr21:44890400-44896600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr21:44890600-44891400	Weak transcription	Fetal Intestine Small	intestine
31	chr21:44890800-44891200	Weak transcription	HepG2	liver
32	chr21:44890800-44892200	Enhancers	Fetal Stomach	stomach
33	chr21:44891000-44891200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr21:44891000-44891200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr21:44891000-44891400	Enhancers	Right Ventricle	heart
36	chr21:44891000-44891800	Active TSS	Stomach Smooth Muscle	stomach
37	chr21:44891000-44892200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr21:44891000-44892400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr21:44891000-44892600	Enhancers	Psoas Muscle	Psoas

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