Variant report

Variant	rs3852147
Chromosome Location	chr5:58780593-58780594
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1156028	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12518641	0.87[JPT][hapmap]
rs1551564	0.86[JPT][hapmap]
rs16889853	0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16889865	0.87[ASN][1000 genomes]
rs16889892	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs174039	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1902610	0.89[ASN][1000 genomes]
rs2112910	0.87[JPT][hapmap]
rs35450986	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41447947	0.87[JPT][hapmap]
rs6870632	0.88[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.90[ASN][1000 genomes]
rs73097356	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704141	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7711639	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs988827	0.90[ASN][1000 genomes]
rs988828	0.88[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap];0.89[ASN][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	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv881707	chr5:58741491-58784102	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58762600-58780600	Weak transcription	Fetal Lung	lung
2	chr5:58774000-58783600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:58774600-58783000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:58776600-58783000	Weak transcription	Fetal Intestine Large	intestine
5	chr5:58777400-58783600	Weak transcription	Psoas Muscle	Psoas
6	chr5:58777800-58781600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:58778600-58783800	Weak transcription	Small Intestine	intestine
8	chr5:58778800-58780600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr5:58778800-58785000	Enhancers	Fetal Brain Male	brain
10	chr5:58779200-58781200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:58779400-58780600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr5:58779400-58780800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:58779400-58780800	Enhancers	HSMMtube	muscle
14	chr5:58779400-58780800	Enhancers	NH-A	brain
15	chr5:58779400-58781600	Enhancers	Rectal Smooth Muscle	rectum
16	chr5:58779400-58782200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:58779400-58782200	Enhancers	Brain Germinal Matrix	brain
18	chr5:58779400-58782200	Enhancers	NHEK	skin
19	chr5:58779400-58784400	Enhancers	Fetal Brain Female	brain
20	chr5:58779400-58784400	Enhancers	Fetal Heart	heart
21	chr5:58779600-58781600	Weak transcription	Liver	Liver
22	chr5:58779600-58781800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr5:58779600-58783600	Weak transcription	Gastric	stomach
24	chr5:58779600-58783600	Weak transcription	Pancreas	Pancrea
25	chr5:58779600-58783600	Enhancers	Hela-S3	cervix
26	chr5:58779800-58781000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:58779800-58781800	Enhancers	Colon Smooth Muscle	Colon
28	chr5:58779800-58783000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:58779800-58783000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:58779800-58783200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:58779800-58783200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr5:58779800-58783600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:58780000-58780600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:58780000-58780600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr5:58780000-58780800	Enhancers	NHDF-Ad	bronchial
36	chr5:58780000-58781200	Flanking Active TSS	A549	lung
37	chr5:58780000-58783600	Weak transcription	Fetal Muscle Leg	muscle
38	chr5:58780200-58780600	Enhancers	Brain Substantia Nigra	brain
39	chr5:58780200-58781000	Enhancers	Brain Cingulate Gyrus	brain
40	chr5:58780200-58781800	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr5:58780200-58782400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:58780400-58780600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:58780400-58780600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr5:58780400-58780600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:58780400-58780800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr5:58780400-58780800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr5:58780400-58781200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:58780400-58781600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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