Variant report

Variant	rs28413740
Chromosome Location	chr3:52352299-52352300
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	chr3:52347614..52350493-chr3:52351552..52354517,2	K562	blood:

Variant related genes	Relation type
ENSG00000114841	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10212380	1.00[EUR][1000 genomes]
rs10212560	1.00[EUR][1000 genomes]
rs10440116	1.00[EUR][1000 genomes]
rs13318570	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052143	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434358	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28636773	1.00[EUR][1000 genomes]
rs34540591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5743834	1.00[EUR][1000 genomes]
rs9813448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813489	1.00[EUR][1000 genomes]
rs9813653	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814016	1.00[EUR][1000 genomes]
rs9815559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9821916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9824342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828432	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828488	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9831689	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9834363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836166	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9842960	1.00[EUR][1000 genomes]
rs9843055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9844178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9845752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9857947	1.00[EUR][1000 genomes]
rs9863874	1.00[EUR][1000 genomes]
rs9868332	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
3	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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	90 gene(s)	inside rSNPs	diseases
4	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
5	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
6	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
7	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
2	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
3	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:52348000-52353600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:52349000-52357200	Weak transcription	HepG2	liver
7	chr3:52350600-52353800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:52350600-52362400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:52351000-52353600	Weak transcription	Liver	Liver
10	chr3:52351200-52352400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr3:52351200-52352400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:52351200-52352400	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:52351200-52352400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr3:52351200-52352600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:52351200-52352600	Enhancers	Fetal Heart	heart
16	chr3:52351200-52352600	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr3:52351200-52352800	Enhancers	Gastric	stomach
18	chr3:52351200-52352800	Enhancers	Spleen	Spleen
19	chr3:52351200-52353200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:52351400-52352600	Enhancers	Primary B cells from cord blood	blood
21	chr3:52351400-52352600	Enhancers	Lung	lung
22	chr3:52351400-52352600	Enhancers	Psoas Muscle	Psoas
23	chr3:52351600-52352400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:52351600-52352400	Active TSS	Brain Anterior Caudate	brain
25	chr3:52351600-52352800	Enhancers	Stomach Mucosa	stomach
26	chr3:52351800-52352600	Enhancers	Primary T cells fromperipheralblood	blood
27	chr3:52351800-52352800	Weak transcription	Primary T cells from cord blood	blood
28	chr3:52351800-52354200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:52352000-52352400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
30	chr3:52352000-52352400	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:52352000-52352400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr3:52352000-52352400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:52352000-52352400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:52352000-52352400	Enhancers	Adipose Nuclei	Adipose
35	chr3:52352000-52352400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr3:52352000-52352400	Enhancers	Placenta	Placenta
37	chr3:52352000-52352400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr3:52352000-52352600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
39	chr3:52352000-52352600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:52352000-52352600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:52352000-52352600	Bivalent Enhancer	Brain Germinal Matrix	brain
42	chr3:52352000-52352600	Enhancers	Fetal Intestine Small	intestine
43	chr3:52352000-52352600	Enhancers	Fetal Muscle Trunk	muscle
44	chr3:52352000-52352600	Bivalent Enhancer	Fetal Stomach	stomach
45	chr3:52352000-52352600	Enhancers	Pancreas	Pancrea
46	chr3:52352000-52352600	Enhancers	Placenta Amnion	Placenta Amnion
47	chr3:52352000-52352600	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr3:52352000-52352600	Enhancers	Right Atrium	heart
49	chr3:52352000-52352600	Enhancers	Right Ventricle	heart
50	chr3:52352000-52352600	Enhancers	NHDF-Ad	bronchial

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