Variant report

Variant	rs6665140
Chromosome Location	chr1:228822928-228822929
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10489542	1.00[CEU][hapmap]
rs12066510	1.00[CEU][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes]
rs12759973	0.94[EUR][1000 genomes]
rs13376515	0.87[EUR][1000 genomes]
rs2180162	1.00[CEU][hapmap]
rs34046190	0.95[EUR][1000 genomes]
rs34813976	0.98[EUR][1000 genomes]
rs35491362	0.98[EUR][1000 genomes]
rs3820265	1.00[CEU][hapmap]
rs4653970	1.00[CHD][hapmap]
rs4654723	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs57678178	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs61825702	0.97[EUR][1000 genomes]
rs6426511	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6678145	1.00[CHD][hapmap]
rs6679936	0.94[EUR][1000 genomes]
rs6692721	0.85[CEU][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes]
rs7544212	0.85[EUR][1000 genomes]
rs7547333	1.00[CEU][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1009511	chr1:228791784-228853665	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2762224	chr1:228791784-228867656	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv945357	chr1:228821805-228824528	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6665140	RNF187	cis	cerebellum	SCAN
rs6665140	TRIM17	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228821000-228823800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:228821000-228823800	Weak transcription	Fetal Lung	lung
3	chr1:228821000-228824000	Weak transcription	Right Atrium	heart
4	chr1:228821200-228823800	Weak transcription	Placenta	Placenta
5	chr1:228822000-228831000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:228822600-228828000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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