Variant report

Variant	rs28540543
Chromosome Location	chr5:16736946-16736947
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16735245..16737580-chr5:16952824..16955569,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10050431	0.85[AFR][1000 genomes]
rs10073942	0.80[AFR][1000 genomes]
rs10074163	0.82[AFR][1000 genomes]
rs11133857	0.93[EUR][1000 genomes]
rs12189316	0.96[EUR][1000 genomes]
rs13356962	0.92[EUR][1000 genomes]
rs13361391	0.82[AFR][1000 genomes]
rs34998371	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899227	0.94[EUR][1000 genomes]
rs72732217	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16730800-16741400	Strong transcription	A549	lung
2	chr5:16730800-16744400	Weak transcription	HSMM	muscle
3	chr5:16733600-16737800	Enhancers	Fetal Kidney	kidney
4	chr5:16734200-16737800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr5:16734600-16744400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:16734800-16737000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:16734800-16739200	Enhancers	Pancreas	Pancrea
8	chr5:16735000-16737000	Flanking Active TSS	Fetal Intestine Small	intestine
9	chr5:16735000-16737800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:16735000-16738600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:16735000-16738600	Enhancers	Fetal Lung	lung
12	chr5:16735000-16739400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:16735000-16739400	Enhancers	Stomach Mucosa	stomach
14	chr5:16735200-16737000	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr5:16735200-16738200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:16735200-16738400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:16735200-16746600	Weak transcription	HSMMtube	muscle
18	chr5:16735400-16737200	Enhancers	Fetal Muscle Leg	muscle
19	chr5:16735400-16737400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr5:16735400-16737800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:16735400-16738000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:16735600-16737200	Flanking Active TSS	Fetal Brain Male	brain
23	chr5:16735600-16737800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:16735600-16738400	Enhancers	NH-A	brain
25	chr5:16735800-16737000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:16735800-16737000	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr5:16735800-16737000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr5:16735800-16738400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:16736000-16737000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:16736000-16737000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:16736000-16737000	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr5:16736000-16737000	Enhancers	NHDF-Ad	bronchial
33	chr5:16736000-16737200	Enhancers	Placenta	Placenta
34	chr5:16736000-16737600	Enhancers	NHLF	lung
35	chr5:16736000-16738200	Bivalent/Poised TSS	HepG2	liver
36	chr5:16736000-16738400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr5:16736000-16738400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:16736000-16738800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr5:16736200-16737000	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr5:16736200-16737400	Enhancers	Osteobl	bone
41	chr5:16736200-16738000	Flanking Active TSS	Fetal Brain Female	brain
42	chr5:16736200-16738400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:16736200-16738400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:16736200-16738400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:16736200-16738600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr5:16736400-16737200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr5:16736400-16737200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr5:16736400-16738800	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr5:16736400-16739200	Enhancers	HMEC	breast
50	chr5:16736400-16740200	Weak transcription	Right Ventricle	heart

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