Variant report

Variant	rs17052401
Chromosome Location	chr3:52775342-52775343
allele	C/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:10)

rs_ID	r²[population]
rs55662247	1.00[AMR][1000 genomes]
rs59277755	1.00[AMR][1000 genomes]
rs6803509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839116	0.89[AFR][1000 genomes]
rs73839117	0.89[AFR][1000 genomes]
rs73839121	1.00[AMR][1000 genomes]
rs73839167	1.00[AMR][1000 genomes]
rs73839179	1.00[AMR][1000 genomes]
rs73839182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73839183	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
2	chr3:52749200-52779800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52749400-52776200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52756200-52777400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:52761600-52781000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:52761600-52802400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:52762000-52787000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:52762600-52776000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:52763800-52788400	Strong transcription	Fetal Brain Female	brain
10	chr3:52763800-52802600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:52764000-52800200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:52764000-52802800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:52764400-52776000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:52764400-52802600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:52764800-52781600	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr3:52764800-52789400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:52765200-52789400	Strong transcription	Adipose Nuclei	Adipose
18	chr3:52765200-52793400	Strong transcription	Fetal Intestine Large	intestine
19	chr3:52765400-52800400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:52765600-52788800	Strong transcription	Brain Anterior Caudate	brain
21	chr3:52765600-52789000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:52765600-52789400	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr3:52766200-52789600	Strong transcription	Placenta	Placenta
24	chr3:52766400-52789400	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:52766400-52802600	Strong transcription	Fetal Thymus	thymus
26	chr3:52767000-52785400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:52767200-52788000	Strong transcription	Brain Germinal Matrix	brain
28	chr3:52767600-52775800	Weak transcription	Spleen	Spleen
29	chr3:52767600-52776200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:52767600-52802600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:52767600-52803400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr3:52767800-52777000	Strong transcription	Liver	Liver
33	chr3:52767800-52777200	Weak transcription	Esophagus	oesophagus
34	chr3:52767800-52777600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:52767800-52779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:52767800-52780200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:52767800-52786000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:52767800-52793000	Weak transcription	Small Intestine	intestine
39	chr3:52767800-52800600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:52768000-52776000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:52768000-52777200	Weak transcription	Right Ventricle	heart
42	chr3:52768000-52777400	Weak transcription	NHLF	lung
43	chr3:52768000-52777600	Weak transcription	Fetal Brain Male	brain
44	chr3:52768000-52785800	Weak transcription	Fetal Heart	heart
45	chr3:52768000-52785800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr3:52768000-52789800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:52768000-52803600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:52768200-52785800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:52768400-52779800	Weak transcription	Gastric	stomach
50	chr3:52768400-52797200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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