Variant report

Variant	rs6948054
Chromosome Location	chr7:136680801-136680802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1158586	0.83[MEX][hapmap]
rs12155015	0.83[MEX][hapmap]
rs12707340	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13242881	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1455860	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1549330	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2061174	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2113545	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2216860	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2350786	0.88[CHD][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.80[MEX][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs324594	0.86[TSI][hapmap]
rs7785096	0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7799047	0.95[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7807871	0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7808355	0.80[ASN][1000 genomes]
rs7809341	0.90[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831147	chr7:136583444-136755741	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2753059	chr7:136633745-136893745	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv528311	chr7:136650607-136680801	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6948054	CHCHD3	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:136666400-136685400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr7:136674800-136694200	Weak transcription	Left Ventricle	heart
3	chr7:136678400-136681400	Weak transcription	Colon Smooth Muscle	Colon
4	chr7:136678400-136685600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:136678600-136681600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:136679000-136681400	Weak transcription	Fetal Heart	heart
7	chr7:136680600-136681400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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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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