Variant report

Variant	rs940347
Chromosome Location	chr7:38110425-38110426
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:10)

rs_ID	r²[population]
rs11972702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357651	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1403988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1524064	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1524068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618737	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3956749	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6956946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963134	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6974574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8074	chr7:37865340-38210087	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv606624	chr7:38067723-38123667	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv887962	chr7:38093233-38203341	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv525236	chr7:38105033-38123667	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs940347	SFRP4	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38108600-38110600	Weak transcription	HSMMtube	muscle
2	chr7:38109800-38110800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:38110000-38110800	Enhancers	Brain Germinal Matrix	brain
4	chr7:38110000-38111000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr7:38110000-38111200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr7:38110200-38111000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr7:38110200-38111000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr7:38110200-38111000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr7:38110200-38111000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:38110200-38111200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr7:38110400-38110800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr7:38110400-38110800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
13	chr7:38110400-38110800	Enhancers	HSMM	muscle
14	chr7:38110400-38111000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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Input of quick search could be:

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

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