Variant report

Variant	rs28544229
Chromosome Location	chr5:68650237-68650238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68649986..68652513-chr5:68664085..68665816,2	MCF-7	breast:
2	chr5:68627053..68629254-chr5:68650186..68651873,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152942	Chromatin interaction
ENSG00000183323	Chromatin interaction
ENSG00000085231	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1006633	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10940223	0.80[EUR][1000 genomes]
rs11948887	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11951429	0.82[AFR][1000 genomes]
rs11952246	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11958576	0.82[AFR][1000 genomes]
rs12654780	0.80[EUR][1000 genomes]
rs12655061	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12658135	0.93[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12659035	0.80[EUR][1000 genomes]
rs1441800	0.80[EUR][1000 genomes]
rs2010354	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs28817404	0.80[EUR][1000 genomes]
rs3756399	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3756400	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3756402	0.93[EUR][1000 genomes]
rs4252221	0.93[EUR][1000 genomes]
rs6871685	0.80[EUR][1000 genomes]
rs6891574	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7730405	0.82[AFR][1000 genomes]
rs7730569	0.82[AFR][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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3515528	chr5:68624487-68653938	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3515529	chr5:68624487-68653938	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv881767	chr5:68625786-68733698	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68638000-68660200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr5:68639200-68663400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:68642200-68650400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:68643000-68664400	Weak transcription	Colonic Mucosa	Colon
5	chr5:68643200-68663200	Weak transcription	Small Intestine	intestine
6	chr5:68643600-68655600	Weak transcription	Fetal Heart	heart
7	chr5:68643800-68660400	Weak transcription	NHEK	skin
8	chr5:68643800-68660800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr5:68643800-68663600	Weak transcription	Brain Angular Gyrus	brain
10	chr5:68644000-68660600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr5:68644200-68652400	Weak transcription	Esophagus	oesophagus
12	chr5:68644200-68660200	Weak transcription	HSMMtube	muscle
13	chr5:68644400-68650600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:68644800-68658200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr5:68644800-68660800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:68645200-68660600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:68645600-68652200	Strong transcription	Adipose Nuclei	Adipose
18	chr5:68645600-68658400	Weak transcription	Gastric	stomach
19	chr5:68645800-68650800	Strong transcription	Primary hematopoietic stem cells	blood
20	chr5:68645800-68651200	Strong transcription	Placenta	Placenta
21	chr5:68645800-68651400	Strong transcription	Fetal Intestine Large	intestine
22	chr5:68645800-68651600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr5:68645800-68651600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:68645800-68652000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:68645800-68652200	Strong transcription	Osteobl	bone
26	chr5:68645800-68652800	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:68645800-68653000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:68645800-68653000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr5:68645800-68653000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:68645800-68653000	Strong transcription	Liver	Liver
31	chr5:68645800-68653200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:68645800-68653200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:68645800-68653200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:68645800-68653200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr5:68645800-68653200	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:68645800-68653200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr5:68645800-68653600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:68645800-68653600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:68645800-68656000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr5:68645800-68660800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr5:68645800-68663400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:68646000-68651400	Strong transcription	Fetal Thymus	thymus
43	chr5:68646000-68651400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr5:68646000-68651600	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr5:68646000-68651800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:68646000-68652200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr5:68646000-68652200	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr5:68646000-68653200	Strong transcription	Primary T cells from cord blood	blood
49	chr5:68646000-68653200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:68646000-68653600	Strong transcription	Dnd41	blood

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