Variant report

Variant	rs2560866
Chromosome Location	chr5:16824846-16824847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs253331	1.00[AMR][1000 genomes]
rs253332	1.00[AMR][1000 genomes]
rs253334	1.00[AMR][1000 genomes]
rs2560863	0.81[AFR][1000 genomes]
rs2625196	1.00[AMR][1000 genomes]
rs2625198	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs31504	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
2	esv3529928	chr5:16748426-16856563	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
3	esv3529929	chr5:16748426-16856563	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv1030550	chr5:16748966-16872084	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv597309	chr5:16791857-16837862	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases
7	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16795200-16829800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:16804400-16827200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:16812600-16829200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:16813800-16828200	Weak transcription	Fetal Intestine Small	intestine
5	chr5:16814200-16828000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:16814400-16826600	Weak transcription	Fetal Stomach	stomach
7	chr5:16818000-16832800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:16818000-16846600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr5:16820000-16841600	Weak transcription	Fetal Kidney	kidney
10	chr5:16820200-16826600	Weak transcription	Fetal Brain Female	brain
11	chr5:16820200-16842600	Weak transcription	HMEC	breast
12	chr5:16820400-16827400	Weak transcription	Placenta	Placenta
13	chr5:16820400-16828000	Weak transcription	Gastric	stomach
14	chr5:16820400-16845400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:16820600-16825200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:16820600-16838800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:16820600-16845000	Weak transcription	NH-A	brain
18	chr5:16820800-16825000	Weak transcription	NHLF	lung
19	chr5:16820800-16825200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr5:16820800-16825400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:16820800-16825600	Weak transcription	Lung	lung
22	chr5:16820800-16826600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:16820800-16826600	Weak transcription	Ovary	ovary
24	chr5:16820800-16826600	Weak transcription	NHDF-Ad	bronchial
25	chr5:16820800-16826600	Weak transcription	NHEK	skin
26	chr5:16820800-16827200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:16820800-16828000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr5:16820800-16829200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:16820800-16834000	Weak transcription	Osteobl	bone
30	chr5:16820800-16843000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:16820800-16855200	Weak transcription	HSMM	muscle
32	chr5:16821600-16826800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:16821800-16826000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:16822600-16828000	Weak transcription	A549	lung
35	chr5:16823600-16835800	Weak transcription	HSMMtube	muscle
36	chr5:16823600-16841600	Weak transcription	HUVEC	blood vessel
37	chr5:16824600-16825200	Weak transcription	Pancreas	Pancrea
38	chr5:16824600-16825600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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