Variant report

Variant	rs1883725
Chromosome Location	chr1:210057927-210057928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210051709..210053987-chr1:210055689..210058098,2	MCF-7	breast:
2	chr1:210053168..210055253-chr1:210056848..210058464,2	MCF-7	breast:
3	chr1:210057678..210059347-chr1:210545335..210547979,2	MCF-7	breast:
4	chr1:210042123..210044687-chr1:210056362..210058775,2	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12025114	0.87[YRI][hapmap]
rs2143545	0.81[EUR][1000 genomes]
rs2206700	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6674507	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6675416	0.92[AMR][1000 genomes]
rs6677876	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6681355	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7511737	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1883725	LOC148696	cis	parietal	SCAN
rs1883725	IL24	cis	cerebellum	SCAN
rs1883725	IL19	cis	cerebellum	SCAN
rs1883725	SERTAD4	cis	cerebellum	SCAN
rs1883725	PFKFB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210053600-210058000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:210053600-210058800	Enhancers	Brain Hippocampus Middle	brain
3	chr1:210055600-210060400	Enhancers	HSMMtube	muscle
4	chr1:210055800-210058400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:210055800-210058400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:210055800-210060000	Weak transcription	Pancreas	Pancrea
7	chr1:210055800-210060200	Enhancers	HSMM	muscle
8	chr1:210056200-210058400	Enhancers	Fetal Brain Female	brain
9	chr1:210056200-210058600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:210056200-210060400	Enhancers	NHEK	skin
11	chr1:210056400-210058000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:210056400-210058400	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:210056400-210058600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:210056400-210058800	Enhancers	HUVEC	blood vessel
15	chr1:210056400-210059000	Enhancers	NHLF	lung
16	chr1:210056400-210059400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:210056400-210059800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:210056400-210060400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:210056400-210060400	Enhancers	HMEC	breast
20	chr1:210056600-210058200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:210056600-210058200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:210056600-210058400	Enhancers	Brain Angular Gyrus	brain
23	chr1:210056600-210058800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr1:210056600-210060000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:210056600-210060200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:210056800-210058600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr1:210056800-210059400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr1:210057000-210058000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:210057000-210058000	Flanking Active TSS	NHDF-Ad	bronchial
30	chr1:210057000-210059200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr1:210057200-210058000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr1:210057200-210058200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:210057200-210058200	Flanking Active TSS	NH-A	brain
34	chr1:210057200-210058600	Flanking Active TSS	Osteobl	bone
35	chr1:210057200-210059800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr1:210057400-210058200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:210057400-210058200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:210057400-210058600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:210057600-210058200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:210057600-210058200	Enhancers	Fetal Intestine Small	intestine
41	chr1:210057600-210058400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:210057600-210058400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr1:210057600-210058600	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr1:210057600-210058600	Enhancers	A549	lung
45	chr1:210057600-210058800	Enhancers	Fetal Intestine Large	intestine
46	chr1:210057800-210058000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:210057800-210058200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr1:210057800-210058200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:210057800-210058200	Flanking Active TSS	Hela-S3	cervix
50	chr1:210057800-210058400	Enhancers	K562	blood

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