Variant report

Variant	rs6604879
Chromosome Location	chr1:224239031-224239032
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10799446	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916201	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12085577	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653642	0.87[ASN][1000 genomes]
rs6604881	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604882	0.82[LWK][hapmap]
rs6688382	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71644767	0.87[ASN][1000 genomes]
rs7515968	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv427941	chr1:224085052-224363163	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv16231	chr1:224204343-224241314	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6604879	TGFB2	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224232400-224240400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:224236000-224240000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:224236000-224240200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:224238200-224240200	Enhancers	HUVEC	blood vessel
5	chr1:224238400-224239200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:224238400-224241400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:224238600-224239800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:224238600-224240000	Weak transcription	NHDF-Ad	bronchial
9	chr1:224238800-224240200	Weak transcription	Osteobl	bone
10	chr1:224238800-224240400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:224238800-224240600	Weak transcription	NHLF	lung
12	chr1:224238800-224242400	Weak transcription	Right Atrium	heart
13	chr1:224238800-224244400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:224239000-224240600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:224239000-224240600	Weak transcription	HMEC	breast
16	chr1:224239000-224241800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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