Variant report

Variant	rs2706786
Chromosome Location	chr4:122660803-122660804
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10001422	0.80[EUR][1000 genomes]
rs10011665	0.80[EUR][1000 genomes]
rs11947643	0.85[EUR][1000 genomes]
rs17051397	0.85[EUR][1000 genomes]
rs17051398	0.87[EUR][1000 genomes]
rs2621219	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2706784	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4077754	0.81[EUR][1000 genomes]
rs4522884	0.87[EUR][1000 genomes]
rs59796939	0.87[EUR][1000 genomes]
rs6825926	0.87[CEU][hapmap]
rs72915905	0.85[EUR][1000 genomes]
rs7661218	0.87[CEU][hapmap];0.87[EUR][1000 genomes]

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	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv461635	chr4:122633535-122720999	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv595357	chr4:122633535-122720999	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2706786	SMCHD1	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122657000-122662200	Weak transcription	Fetal Brain Male	brain
2	chr4:122657600-122663200	Enhancers	Fetal Lung	lung
3	chr4:122657800-122661600	Enhancers	HSMM	muscle
4	chr4:122658000-122662800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:122658200-122661200	Enhancers	Fetal Stomach	stomach
6	chr4:122659200-122661200	Enhancers	Fetal Muscle Leg	muscle
7	chr4:122659600-122661200	Enhancers	Fetal Kidney	kidney
8	chr4:122659600-122661400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr4:122659600-122661600	Enhancers	HSMMtube	muscle
10	chr4:122660200-122661000	Weak transcription	Placenta	Placenta
11	chr4:122660200-122661400	Flanking Active TSS	Fetal Heart	heart
12	chr4:122660400-122661200	Enhancers	Ovary	ovary
13	chr4:122660400-122661200	Enhancers	Right Atrium	heart
14	chr4:122660600-122662600	Weak transcription	Fetal Brain Female	brain
15	chr4:122660800-122661200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:122660800-122661400	Enhancers	NHLF	lung

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

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