Variant report

Variant	rs729555
Chromosome Location	chr3:52478389-52478390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52467987..52470484-chr3:52476648..52478461,2	K562	blood:
2	chr3:52310738..52313208-chr3:52476812..52479185,3	K562	blood:
3	chr3:52310738..52312767-chr3:52476812..52478941,2	K562	blood:

Variant related genes	Relation type
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10460962	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10461027	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10461028	0.80[EUR][1000 genomes]
rs10865971	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11706515	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11707056	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11708581	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs11708811	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11710014	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11711974	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11713914	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11714358	0.82[EUR][1000 genomes]
rs11715208	0.82[EUR][1000 genomes]
rs11715391	1.00[CEU][hapmap]
rs11716487	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11717028	0.85[EUR][1000 genomes]
rs11720365	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11721277	0.88[EUR][1000 genomes]
rs1319202	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17052051	1.00[CEU][hapmap]
rs17052052	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17052053	0.91[CEU][hapmap]
rs17052054	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17263770	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1767	0.91[CEU][hapmap]
rs1769	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs35976326	0.82[EUR][1000 genomes]
rs3733063	0.91[CEU][hapmap]
rs3886875	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs55676974	0.82[EUR][1000 genomes]
rs55806905	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55813842	0.88[EUR][1000 genomes]
rs56002041	0.88[EUR][1000 genomes]
rs56322342	0.88[EUR][1000 genomes]
rs56899118	0.88[EUR][1000 genomes]
rs57849650	0.88[EUR][1000 genomes]
rs61644644	0.82[EUR][1000 genomes]
rs6445385	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6776759	0.92[EUR][1000 genomes]
rs6783652	0.82[EUR][1000 genomes]
rs6793317	0.91[CEU][hapmap]
rs724801	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73072990	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088791	0.82[EUR][1000 genomes]
rs73091166	0.88[EUR][1000 genomes]
rs73091168	0.88[EUR][1000 genomes]
rs746239	0.88[EUR][1000 genomes]
rs7615405	0.85[EUR][1000 genomes]
rs7633687	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7643913	0.86[CEU][hapmap];0.82[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	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	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
3	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
4	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
5	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
6	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
7	nsv590303	chr3:52469785-52478428	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52450200-52478400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:52470800-52484200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:52472200-52478600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:52472600-52478400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:52475200-52478400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:52475800-52478800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:52476200-52479400	Active TSS	Brain Anterior Caudate	brain
8	chr3:52476400-52478600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:52476600-52479600	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr3:52476800-52478400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:52476800-52478600	Active TSS	Stomach Smooth Muscle	stomach
12	chr3:52476800-52479200	Active TSS	Left Ventricle	heart
13	chr3:52476800-52479600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr3:52477200-52478400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr3:52477200-52478400	Weak transcription	Colonic Mucosa	Colon
16	chr3:52477200-52479200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:52477200-52479200	Flanking Active TSS	Placenta	Placenta
18	chr3:52477400-52479000	Active TSS	Brain Hippocampus Middle	brain
19	chr3:52477400-52479000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:52477400-52479000	Flanking Active TSS	Fetal Muscle Leg	muscle
21	chr3:52477600-52478400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr3:52477600-52478400	Active TSS	Lung	lung
23	chr3:52477600-52478400	Enhancers	HUVEC	blood vessel
24	chr3:52477600-52479200	Active TSS	Psoas Muscle	Psoas
25	chr3:52477800-52478400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:52477800-52478400	Active TSS	Pancreas	Pancrea
27	chr3:52477800-52478800	Flanking Active TSS	HepG2	liver
28	chr3:52477800-52480800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:52478000-52478400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:52478000-52478400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr3:52478000-52478400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
32	chr3:52478000-52478600	Active TSS	Right Atrium	heart
33	chr3:52478000-52479000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:52478000-52479400	Enhancers	Esophagus	oesophagus
35	chr3:52478200-52478400	Bivalent/Poised TSS	Fetal Stomach	stomach
36	chr3:52478200-52478600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:52478200-52478800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:52478200-52479000	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr3:52478200-52479000	Flanking Active TSS	Spleen	Spleen
40	chr3:52478200-52479200	Flanking Active TSS	Right Ventricle	heart
41	chr3:52478200-52479400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:52478200-52479400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr3:52478200-52479400	Flanking Active TSS	Hela-S3	cervix
44	chr3:52478200-52479600	Enhancers	Gastric	stomach
45	chr3:52478200-52484000	Enhancers	Fetal Heart	heart

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