Variant report

Variant	rs56259931
Chromosome Location	chr3:52574365-52574366
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	chr3:52536407..52539525-chr3:52571038..52574825,3	K562	blood:

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]
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]
rs57319306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:126 , 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	chr3:52572200-52574400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:52572200-52574600	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr3:52572200-52575200	Weak transcription	Fetal Kidney	kidney
5	chr3:52572200-52581000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:52572200-52584400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:52572400-52574400	Enhancers	Adipose Nuclei	Adipose
8	chr3:52572400-52578800	Weak transcription	A549	lung
9	chr3:52572400-52580600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:52572400-52581800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:52572400-52594200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:52572400-52633000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:52572600-52574600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:52573000-52574800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:52573000-52574800	Genic enhancers	GM12878-XiMat	blood
16	chr3:52573000-52575000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:52573000-52575400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:52573200-52574400	Weak transcription	Brain Substantia Nigra	brain
19	chr3:52573200-52575000	Weak transcription	Brain Angular Gyrus	brain
20	chr3:52573200-52575000	Weak transcription	Fetal Intestine Large	intestine
21	chr3:52573200-52575600	Weak transcription	Fetal Lung	lung
22	chr3:52573200-52576200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:52573200-52576400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:52573200-52576600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:52573200-52578600	Weak transcription	Brain Germinal Matrix	brain
26	chr3:52573200-52579000	Weak transcription	Thymus	Thymus
27	chr3:52573200-52582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:52573200-52583400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:52573200-52585000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:52573200-52586400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:52573200-52589600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:52573200-52590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:52573400-52574400	Weak transcription	HMEC	breast
34	chr3:52573400-52574800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:52573400-52574800	Weak transcription	Fetal Thymus	thymus
36	chr3:52573400-52575000	Weak transcription	Primary B cells from cord blood	blood
37	chr3:52573400-52575000	Weak transcription	Fetal Heart	heart
38	chr3:52573400-52575000	Weak transcription	HSMMtube	muscle
39	chr3:52573400-52575600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:52573400-52575800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:52573400-52575800	Strong transcription	NHDF-Ad	bronchial
42	chr3:52573400-52576000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:52573400-52576000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:52573400-52576200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:52573400-52576200	Strong transcription	NHLF	lung
46	chr3:52573400-52580600	Weak transcription	Fetal Brain Male	brain
47	chr3:52573400-52585200	Weak transcription	Small Intestine	intestine
48	chr3:52573400-52595000	Weak transcription	Stomach Mucosa	stomach
49	chr3:52573600-52574400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:52573600-52574400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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