Variant report

Variant	rs57319306
Chromosome Location	chr3:52575251-52575252
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	chr3:52574434..52577960-chr3:52578839..52582098,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NT5DC2-1	chr3:52573952-52575907	ENSG00000245797

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10510759	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1987234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34173244	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs35920544	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	0.84[AFR][1000 genomes]
rs56259931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56960576	1.00[EUR][1000 genomes]
rs57008939	0.84[AFR][1000 genomes]
rs57246324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57298447	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57560655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57757646	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs57869735	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs58100002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58725214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58924550	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60311166	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60415551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60611300	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60682984	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60823713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60916588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61220667	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61538294	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6445536	0.85[AMR][1000 genomes]
rs6780005	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72947535	0.96[AFR][1000 genomes]
rs72947580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947583	1.00[EUR][1000 genomes]
rs72947584	1.00[EUR][1000 genomes]
rs72947589	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950430	0.85[AFR][1000 genomes]
rs72950432	0.83[AFR][1000 genomes]
rs72960240	0.85[AMR][1000 genomes]
rs72960281	0.85[AMR][1000 genomes]
rs72965177	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72965181	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73837804	1.00[EUR][1000 genomes]
rs7619643	0.85[AMR][1000 genomes]
rs7647992	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7648016	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52571400-52594200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:52572200-52581000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:52572200-52584400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:52572400-52578800	Weak transcription	A549	lung
5	chr3:52572400-52580600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:52572400-52581800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:52572400-52594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:52573000-52575400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:52573200-52575600	Weak transcription	Fetal Lung	lung
11	chr3:52573200-52576200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:52573200-52576400	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:52573200-52576600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:52573200-52578600	Weak transcription	Brain Germinal Matrix	brain
15	chr3:52573200-52579000	Weak transcription	Thymus	Thymus
16	chr3:52573200-52582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:52573200-52583400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:52573200-52585000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:52573200-52586400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:52573200-52589600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:52573200-52590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:52573400-52575600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:52573400-52575800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:52573400-52575800	Strong transcription	NHDF-Ad	bronchial
25	chr3:52573400-52576000	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:52573400-52576000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:52573400-52576200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:52573400-52576200	Strong transcription	NHLF	lung
29	chr3:52573400-52580600	Weak transcription	Fetal Brain Male	brain
30	chr3:52573400-52585200	Weak transcription	Small Intestine	intestine
31	chr3:52573400-52595000	Weak transcription	Stomach Mucosa	stomach
32	chr3:52573600-52575800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:52573600-52575800	Strong transcription	HepG2	liver
34	chr3:52573600-52575800	Strong transcription	Osteobl	bone
35	chr3:52573600-52576000	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:52573600-52576000	Strong transcription	HSMM	muscle
37	chr3:52573600-52576200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:52573600-52576200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:52573600-52576200	Strong transcription	Fetal Muscle Leg	muscle
40	chr3:52573600-52576400	Strong transcription	NHEK	skin
41	chr3:52573600-52577600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:52573600-52578400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:52573600-52578600	Weak transcription	Aorta	Aorta
44	chr3:52573600-52578800	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:52573600-52578800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:52573600-52578800	Weak transcription	Fetal Brain Female	brain
47	chr3:52573600-52580600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:52573600-52580600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:52573600-52581200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr3:52573600-52581200	Weak transcription	Esophagus	oesophagus

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