Variant report

Variant	rs3746952
Chromosome Location	chr21:44887247-44887248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:44887100-44887250	HBMEC	blood vessel:	n/a	chr21:44887194-44887207
2	CTCF	chr21:44887180-44887330	HBMEC	blood vessel:	n/a	chr21:44887194-44887207
3	RUNX3	chr21:44887208-44888169	GM12878	blood:	n/a	chr21:44887850-44887865 chr21:44887913-44887928 chr21:44887883-44887898
4	CTCF	chr21:44887180-44887330	HAc	cerebellar:	n/a	chr21:44887194-44887207
5	CTCF	chr21:44887160-44887310	HRPEpiC	eye:	n/a	chr21:44887194-44887207
6	CTCF	chr21:44887120-44887270	HCPEpiC	choroid plexus:	n/a	chr21:44887194-44887207
7	CTCF	chr21:44887160-44887310	HUVEC	blood vessel:	n/a	chr21:44887194-44887207

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:44885660..44888492-chr21:44912616..44914630,3	MCF-7	breast:
2	chr21:44886960..44890249-chr21:44891920..44896303,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RRP1B-2	chr21:44886938-44887755	XLOC_013965
2	lnc-RRP1B-2	chr21:44886938-44888633	NONHSAT082423
3	lnc-SIK1-4	chr21:44886902-44887491	NONHSAT082425

Variant related genes	Relation type
LINC00313	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs9982658	1.00[JPT][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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44879000-44889200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr21:44879400-44889400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr21:44880600-44890800	Enhancers	HepG2	liver
4	chr21:44882600-44891200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr21:44882800-44887600	Enhancers	Placenta	Placenta
6	chr21:44883400-44889800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:44884000-44888200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr21:44884000-44889000	Weak transcription	Esophagus	oesophagus
9	chr21:44884000-44891000	Weak transcription	Psoas Muscle	Psoas
10	chr21:44884200-44888800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr21:44884400-44887600	Weak transcription	Right Atrium	heart
12	chr21:44884800-44887600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr21:44884800-44887800	Weak transcription	Gastric	stomach
14	chr21:44884800-44890800	Weak transcription	Fetal Stomach	stomach
15	chr21:44885400-44887800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr21:44885600-44894000	Weak transcription	Hela-S3	cervix
17	chr21:44886200-44887400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr21:44886200-44887400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr21:44886200-44887400	Enhancers	HSMM	muscle
20	chr21:44886200-44887400	Enhancers	HSMMtube	muscle
21	chr21:44886200-44887600	Weak transcription	Pancreas	Pancrea
22	chr21:44886200-44887800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr21:44886400-44887400	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr21:44886400-44887400	Weak transcription	Lung	lung
25	chr21:44886400-44887600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr21:44886400-44887800	Weak transcription	Fetal Intestine Small	intestine
27	chr21:44886400-44888000	Weak transcription	Fetal Intestine Large	intestine
28	chr21:44886400-44888200	Weak transcription	Stomach Mucosa	stomach
29	chr21:44886600-44887800	Enhancers	NH-A	brain
30	chr21:44886800-44887400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr21:44886800-44887600	Enhancers	Fetal Lung	lung
32	chr21:44887000-44887400	Enhancers	Osteobl	bone
33	chr21:44887000-44887600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr21:44887000-44887800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr21:44887000-44888000	Enhancers	A549	lung
36	chr21:44887200-44887400	Flanking Active TSS	Spleen	Spleen
37	chr21:44887200-44887600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr21:44887200-44887800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr21:44887200-44888000	Enhancers	HUVEC	blood vessel
40	chr21:44887200-44888200	Enhancers	Brain Inferior Temporal Lobe	brain

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