Variant report

Variant	rs4658241
Chromosome Location	chr1:92066310-92066311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10493855	1.00[ASN][1000 genomes]
rs17131500	1.00[ASN][1000 genomes]
rs17503335	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4658238	0.92[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs4658243	0.84[EUR][1000 genomes]
rs56034708	0.93[ASN][1000 genomes]
rs58841613	0.89[ASN][1000 genomes]
rs6604046	1.00[CEU][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6659090	0.84[EUR][1000 genomes]

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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv946071	chr1:92060669-92067233	Weak transcription Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4658241	CCBL2	cis	cerebellum	SCAN
rs4658241	TGFBR3	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92051800-92067600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:92055800-92076400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:92057200-92070400	Weak transcription	Psoas Muscle	Psoas
4	chr1:92059600-92067200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:92059800-92068800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:92060600-92067200	Weak transcription	Lung	lung
7	chr1:92060600-92070200	Weak transcription	Right Ventricle	heart
8	chr1:92060800-92066400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:92060800-92066400	Weak transcription	Right Atrium	heart
10	chr1:92060800-92067200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:92060800-92067600	Weak transcription	Left Ventricle	heart
12	chr1:92060800-92070200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:92061200-92070000	Weak transcription	Ovary	ovary
14	chr1:92062400-92074200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:92063200-92067800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:92064000-92070000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:92064600-92066400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:92064800-92066400	Weak transcription	Placenta	Placenta
19	chr1:92065400-92068400	Enhancers	Fetal Heart	heart
20	chr1:92066000-92069200	Enhancers	NHDF-Ad	bronchial
21	chr1:92066200-92066400	Enhancers	Fetal Kidney	kidney
22	chr1:92066200-92068000	Enhancers	K562	blood
23	chr1:92066200-92068200	Enhancers	Fetal Stomach	stomach

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