Variant report

Variant	rs28452990
Chromosome Location	chr3:51505285-51505286
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	chr3:51503705..51505544-chr3:51532153..51534269,2	K562	blood:

Variant related genes	Relation type
ENSG00000145041	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs12330534	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13314120	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13321674	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13433729	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051799	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051832	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17081501	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28421789	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28457212	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28653367	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2883900	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549265	1.00[AMR][1000 genomes]
rs56942057	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61737032	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951441	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953417	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953419	1.00[ASN][1000 genomes]
rs72953421	1.00[ASN][1000 genomes]
rs72953423	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953429	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7627636	1.00[ASN][1000 genomes]
rs904144	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9311470	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9808940	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9809757	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812008	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815684	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816075	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824779	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826664	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827665	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9827917	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838294	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839516	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839608	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840331	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9842066	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855809	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857893	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858497	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9864213	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9864952	1.00[ASN][1000 genomes]
rs9866513	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866604	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870147	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880050	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	1.00[AMR][1000 genomes]
rs9882601	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51458200-51515000	Weak transcription	Fetal Brain Male	brain
2	chr3:51467800-51524000	Weak transcription	Small Intestine	intestine
3	chr3:51476000-51506000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:51477200-51515000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:51490400-51515000	Weak transcription	Stomach Mucosa	stomach
6	chr3:51491400-51532800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:51495000-51532600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:51495400-51505800	Weak transcription	NHLF	lung
9	chr3:51495400-51513200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:51495600-51505800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:51495600-51508800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:51495600-51509600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:51495600-51509600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:51495800-51505800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:51495800-51506600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:51495800-51506600	Strong transcription	Adipose Nuclei	Adipose
17	chr3:51495800-51507000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:51495800-51508400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:51495800-51508800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr3:51495800-51510400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:51495800-51510400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr3:51495800-51510400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:51495800-51510600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:51495800-51518200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr3:51495800-51518200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:51495800-51526800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:51495800-51531800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:51496000-51506000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:51496000-51517800	Strong transcription	Fetal Muscle Trunk	muscle
30	chr3:51496000-51518400	Strong transcription	Fetal Stomach	stomach
31	chr3:51496000-51531800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:51496200-51506600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:51496200-51506600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:51496200-51506800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:51496200-51506800	Strong transcription	Primary B cells from cord blood	blood
36	chr3:51496200-51506800	Strong transcription	Primary T cells from cord blood	blood
37	chr3:51496200-51506800	Strong transcription	Liver	Liver
38	chr3:51496200-51507200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:51496200-51507800	Strong transcription	Fetal Thymus	thymus
40	chr3:51496200-51509000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:51496200-51509600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:51496200-51510200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:51496200-51516600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:51496200-51516800	Strong transcription	Dnd41	blood
45	chr3:51496200-51518000	Strong transcription	Placenta	Placenta
46	chr3:51496200-51530600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:51496200-51531000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:51496400-51506000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr3:51496400-51525800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:51497000-51508200	Strong transcription	Stomach Smooth Muscle	stomach

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