Variant report

Variant	rs6554944
Chromosome Location	chr5:16726283-16726284
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16723548..16725058-chr5:16725138..16727326,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10073942	1.00[CHB][hapmap]
rs10074163	1.00[CHB][hapmap]
rs11747522	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3860136	1.00[CHB][hapmap]
rs4702164	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72750521	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869660	chr5:16651289-16766428	Genic enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv880373	chr5:16710572-16785604	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16682400-16736000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:16711200-16736400	Weak transcription	Hela-S3	cervix
3	chr5:16711400-16727800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:16711400-16728200	Weak transcription	Spleen	Spleen
5	chr5:16711400-16730200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:16711400-16731800	Weak transcription	HMEC	breast
7	chr5:16711600-16736000	Weak transcription	Placenta	Placenta
8	chr5:16713800-16731600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:16713800-16735600	Weak transcription	Colonic Mucosa	Colon
10	chr5:16714000-16730200	Weak transcription	Osteobl	bone
11	chr5:16714200-16730400	Weak transcription	NHLF	lung
12	chr5:16714200-16736000	Weak transcription	NHDF-Ad	bronchial
13	chr5:16714400-16730000	Weak transcription	NH-A	brain
14	chr5:16714600-16726400	Weak transcription	Brain Substantia Nigra	brain
15	chr5:16714600-16728200	Weak transcription	Psoas Muscle	Psoas
16	chr5:16722200-16730200	Weak transcription	Stomach Mucosa	stomach
17	chr5:16722200-16734200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:16722400-16726400	Weak transcription	Gastric	stomach
19	chr5:16722400-16726800	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:16722400-16728000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:16722400-16728000	Weak transcription	Brain Angular Gyrus	brain
22	chr5:16722400-16728000	Weak transcription	Lung	lung
23	chr5:16722400-16728000	Weak transcription	Pancreas	Pancrea
24	chr5:16722400-16728200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:16722400-16729800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr5:16722400-16730000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:16722400-16730000	Weak transcription	NHEK	skin
28	chr5:16722400-16730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:16722400-16734000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:16722600-16726600	Weak transcription	Fetal Brain Female	brain
31	chr5:16722600-16727800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:16722600-16728200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:16722600-16736000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr5:16722800-16727800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:16722800-16728000	Weak transcription	HepG2	liver
36	chr5:16723000-16726400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:16723400-16735600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:16724000-16728000	Weak transcription	Right Ventricle	heart
39	chr5:16724400-16726600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr5:16724400-16726600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:16724400-16726600	Weak transcription	Fetal Muscle Leg	muscle
42	chr5:16724400-16728000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr5:16724600-16734800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:16724800-16726400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:16724800-16727800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:16724800-16728800	Weak transcription	Fetal Intestine Large	intestine
47	chr5:16725000-16727800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:16725000-16728000	Weak transcription	Ovary	ovary
49	chr5:16725400-16726400	Enhancers	HUVEC	blood vessel
50	chr5:16725400-16726800	Strong transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links