Variant report

Variant	rs1509288
Chromosome Location	chr4:126309456-126309457
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10012726	1.00[AMR][1000 genomes]
rs10025691	0.83[YRI][hapmap]
rs10084893	0.83[YRI][hapmap]
rs10857105	0.81[AFR][1000 genomes]
rs11733424	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11932005	0.83[YRI][hapmap]
rs11942648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12640965	0.83[YRI][hapmap]
rs12711125	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13144799	0.83[YRI][hapmap]
rs13144803	0.83[YRI][hapmap]
rs1396700	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1509293	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1509294	0.81[AFR][1000 genomes]
rs1509295	0.81[AFR][1000 genomes]
rs1509296	0.81[AFR][1000 genomes]
rs1509297	0.81[AFR][1000 genomes]
rs1509298	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1509301	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1605825	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1605826	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1605827	0.81[AFR][1000 genomes]
rs2055768	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2102461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2135427	0.83[YRI][hapmap]
rs2135428	0.83[YRI][hapmap]
rs2390841	0.83[YRI][hapmap]
rs2457262	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2663253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2663258	1.00[AMR][1000 genomes]
rs2663262	1.00[AMR][1000 genomes]
rs2663284	1.00[AMR][1000 genomes]
rs2710537	1.00[AMR][1000 genomes]
rs2710565	1.00[AMR][1000 genomes]
rs2710577	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710585	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710586	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710588	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710589	0.83[YRI][hapmap]
rs28470542	1.00[AMR][1000 genomes]
rs28871071	1.00[AMR][1000 genomes]
rs4508902	0.83[YRI][hapmap]
rs4834029	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4834030	0.83[YRI][hapmap]
rs4834034	0.83[YRI][hapmap]
rs4834036	0.83[YRI][hapmap]
rs4834039	0.83[YRI][hapmap]
rs4834041	0.83[YRI][hapmap]
rs4834047	0.83[YRI][hapmap]
rs6534480	0.83[YRI][hapmap]
rs6534484	0.83[YRI][hapmap]
rs6833240	0.83[YRI][hapmap]
rs6844307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7660088	0.81[AFR][1000 genomes]
rs7660325	0.81[AFR][1000 genomes]
rs7667605	0.83[YRI][hapmap]
rs7675556	0.83[YRI][hapmap]
rs7683955	0.83[YRI][hapmap]
rs906793	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs906794	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs925244	1.00[AMR][1000 genomes]
rs958845	0.83[YRI][hapmap]
rs988863	0.83[YRI][hapmap]
rs988933	0.83[YRI][hapmap]
rs9968423	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006068	chr4:126103233-126497467	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830051	chr4:126234895-126403426	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv470070	chr4:126299145-126408586	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:126290800-126317600	Weak transcription	Fetal Brain Male	brain
2	chr4:126296000-126311200	Weak transcription	Aorta	Aorta
3	chr4:126304200-126309600	Weak transcription	Fetal Heart	heart
4	chr4:126305000-126310600	Weak transcription	Fetal Kidney	kidney
5	chr4:126305400-126309800	Weak transcription	Fetal Lung	lung
6	chr4:126308200-126309600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:126308400-126336000	Weak transcription	Left Ventricle	heart
8	chr4:126308600-126311000	Enhancers	Osteobl	bone
9	chr4:126308800-126309800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:126308800-126311200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:126308800-126311200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:126309000-126310400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr4:126309000-126311200	Enhancers	NHDF-Ad	bronchial
14	chr4:126309000-126311400	Enhancers	NHLF	lung
15	chr4:126309000-126312000	Enhancers	Colon Smooth Muscle	Colon
16	chr4:126309200-126309800	Enhancers	HUVEC	blood vessel
17	chr4:126309200-126310200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:126309200-126310600	Enhancers	HSMM	muscle
19	chr4:126309200-126310800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr4:126309200-126311000	Enhancers	Adipose Nuclei	Adipose
21	chr4:126309200-126311200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:126309200-126311200	Enhancers	HSMMtube	muscle
23	chr4:126309200-126311400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:126309200-126311400	Weak transcription	Brain Substantia Nigra	brain
25	chr4:126309200-126312000	Enhancers	Rectal Smooth Muscle	rectum
26	chr4:126309400-126309800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:126309400-126311200	Enhancers	NH-A	brain
28	chr4:126309400-126311400	Weak transcription	Fetal Stomach	stomach

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