Variant report

Variant	rs555860
Chromosome Location	chr22:27592742-27592743
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs491735	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs492416	0.95[CEU][hapmap];0.94[CHB][hapmap];0.98[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs494604	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497365	0.91[ASN][1000 genomes]
rs497368	0.91[ASN][1000 genomes]
rs499712	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs499733	0.90[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs500281	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530536	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs561417	0.91[ASN][1000 genomes]
rs849449	0.90[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs864754	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9613395	0.94[CEU][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	nsv917333	chr22:26931825-27692024	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	142 gene(s)	inside rSNPs	diseases
2	esv34168	chr22:27289097-27678031	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs555860	CCDC116	cis	cerebellum	SCAN
rs555860	SEZ6L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27571800-27598600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:27588600-27598800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:27588800-27597600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr22:27588800-27599000	Weak transcription	Aorta	Aorta
5	chr22:27590200-27594600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr22:27590200-27597400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr22:27590400-27593600	Enhancers	Fetal Stomach	stomach
8	chr22:27590600-27597600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr22:27591400-27593000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr22:27591400-27593400	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr22:27591600-27593200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr22:27591600-27597200	Weak transcription	Fetal Brain Female	brain
13	chr22:27591800-27594600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr22:27591800-27596400	Weak transcription	Fetal Brain Male	brain
15	chr22:27591800-27597800	Weak transcription	HSMMtube	muscle
16	chr22:27592000-27593200	Weak transcription	Stomach Smooth Muscle	stomach

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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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