Variant report

Variant	rs9873175
Chromosome Location	chr3:52059636-52059637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52059478..52062079-chr3:52187241..52190145,3	K562	blood:
2	chr3:52058192..52060960-chr3:52064469..52066894,2	K562	blood:
3	chr3:52053407..52057032-chr3:52057873..52061894,4	K562	blood:

Variant related genes	Relation type
ENSG00000164087	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12489539	0.86[MEX][hapmap]
rs12492696	0.80[AMR][1000 genomes]
rs12493204	0.86[MEX][hapmap]
rs17051963	0.86[MEX][hapmap]
rs3821841	0.91[MEX][hapmap]
rs4687606	0.80[AMR][1000 genomes]
rs4687608	0.91[MEX][hapmap]
rs4687609	0.82[MEX][hapmap]
rs4687798	0.95[MEX][hapmap]
rs4687801	0.82[MEX][hapmap]
rs4687806	0.86[MEX][hapmap]
rs4687809	0.86[MEX][hapmap]
rs66514320	0.87[AMR][1000 genomes]
rs7618573	0.86[MEX][hapmap]
rs920160	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
4	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	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
9	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	esv3398903	chr3:52056112-52061110	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52046200-52060600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr3:52048600-52061000	Enhancers	Fetal Muscle Leg	muscle
3	chr3:52050600-52073400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:52053000-52060400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:52054600-52060600	Enhancers	Lung	lung
6	chr3:52055600-52060800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr3:52055800-52060600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:52055800-52060800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr3:52056000-52062400	Weak transcription	NHEK	skin
10	chr3:52056600-52064400	Weak transcription	Pancreas	Pancrea
11	chr3:52056600-52066400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:52056800-52060400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:52057200-52060000	Enhancers	GM12878-XiMat	blood
14	chr3:52057400-52060200	Weak transcription	Fetal Brain Female	brain
15	chr3:52057400-52060600	Enhancers	Psoas Muscle	Psoas
16	chr3:52057600-52060000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:52057600-52060200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:52057800-52060000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:52057800-52060000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:52057800-52060000	Weak transcription	Fetal Brain Male	brain
21	chr3:52057800-52062600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:52057800-52062800	Weak transcription	Osteobl	bone
23	chr3:52058000-52062400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:52058000-52062400	Enhancers	Fetal Muscle Trunk	muscle
25	chr3:52058000-52062600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:52058000-52062600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:52058400-52059800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:52058400-52060400	Enhancers	Right Ventricle	heart
29	chr3:52058400-52060800	Enhancers	Left Ventricle	heart
30	chr3:52058400-52060800	Enhancers	Right Atrium	heart
31	chr3:52058400-52062400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:52058600-52062200	Weak transcription	NHDF-Ad	bronchial
33	chr3:52058600-52062400	Weak transcription	K562	blood
34	chr3:52059000-52060600	Enhancers	Brain Cingulate Gyrus	brain
35	chr3:52059000-52060600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr3:52059200-52060000	Weak transcription	Colonic Mucosa	Colon
37	chr3:52059200-52060400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:52059200-52060600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:52059200-52060600	Enhancers	Brain Substantia Nigra	brain
40	chr3:52059200-52060800	Enhancers	Spleen	Spleen
41	chr3:52059200-52062600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:52059400-52060200	Enhancers	Aorta	Aorta
43	chr3:52059400-52060200	Bivalent Enhancer	Fetal Stomach	stomach
44	chr3:52059400-52060600	Enhancers	Brain Angular Gyrus	brain
45	chr3:52059400-52060600	Enhancers	HSMMtube	muscle
46	chr3:52059600-52059800	Enhancers	Esophagus	oesophagus
47	chr3:52059600-52060000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:52059600-52060200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:52059600-52060400	Enhancers	Brain Anterior Caudate	brain
50	chr3:52059600-52060600	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links