Variant report

Variant	rs16869688
Chromosome Location	chr5:17306610-17306611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:17298640..17300836-chr5:17306560..17308116,2	MCF-7	breast:
2	chr5:17215446..17220855-chr5:17303141..17309835,13	MCF-7	breast:
3	chr5:17215544..17223113-chr5:17298591..17308160,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176788	Chromatin interaction
ENSG00000215196	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10075136	0.96[ASN][1000 genomes]
rs11949223	0.94[ASN][1000 genomes]
rs11949279	0.94[ASN][1000 genomes]
rs16869690	0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16869693	0.92[ASN][1000 genomes]
rs2134242	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs2173968	0.90[JPT][hapmap]
rs2459811	0.81[GIH][hapmap]
rs2650923	0.90[JPT][hapmap]
rs2650943	0.90[JPT][hapmap]
rs2650944	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs2650945	0.89[JPT][hapmap]
rs2652643	0.86[JPT][hapmap]
rs2652645	0.89[JPT][hapmap]
rs2652647	0.90[JPT][hapmap]
rs28665339	0.94[ASN][1000 genomes]
rs298547	0.81[GIH][hapmap]
rs298558	0.81[GIH][hapmap];0.90[JPT][hapmap]
rs298560	0.90[JPT][hapmap]
rs60344534	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6874823	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052845	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv515766	chr5:17283367-17306790	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv461988	chr5:17296342-17484038	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv597313	chr5:17296342-17484038	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17302000-17307000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr5:17304000-17306800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:17304200-17306800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:17304200-17306800	Enhancers	Muscle Satellite Cultured Cells	--
5	chr5:17304200-17307000	Flanking Active TSS	Hela-S3	cervix
6	chr5:17304400-17307000	Enhancers	NH-A	brain
7	chr5:17305000-17307000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:17305400-17307000	Enhancers	Stomach Mucosa	stomach
9	chr5:17305800-17307400	Enhancers	Placenta	Placenta
10	chr5:17306000-17306800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:17306000-17306800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:17306000-17306800	Enhancers	Rectal Mucosa Donor 29	rectum
13	chr5:17306000-17307000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:17306000-17307000	Enhancers	HMEC	breast
15	chr5:17306200-17306800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:17306200-17306800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:17306200-17306800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:17306200-17306800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:17306200-17307000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:17306200-17307200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:17306200-17315200	Weak transcription	NHLF	lung
22	chr5:17306400-17306800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:17306400-17306800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:17306400-17306800	Enhancers	Ovary	ovary
25	chr5:17306400-17306800	Flanking Active TSS	Osteobl	bone
26	chr5:17306400-17307000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr5:17306400-17307000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:17306400-17307000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:17306400-17307000	Enhancers	Esophagus	oesophagus
30	chr5:17306400-17307000	Enhancers	Fetal Muscle Trunk	muscle
31	chr5:17306400-17307000	Enhancers	Lung	lung
32	chr5:17306400-17307000	Enhancers	Pancreas	Pancrea
33	chr5:17306400-17307000	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr5:17306600-17306800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr5:17306600-17306800	Flanking Active TSS	A549	lung
36	chr5:17306600-17307000	Enhancers	Aorta	Aorta
37	chr5:17306600-17307000	Enhancers	Colonic Mucosa	Colon
38	chr5:17306600-17307000	Enhancers	Fetal Intestine Large	intestine
39	chr5:17306600-17307000	Enhancers	Gastric	stomach
40	chr5:17306600-17307000	Enhancers	NHEK	skin
41	chr5:17306600-17307200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links