Variant report

Variant	rs7291247
Chromosome Location	chr22:27809402-27809403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs16984543	0.98[ASN][1000 genomes]
rs5752539	0.86[EUR][1000 genomes]
rs5752540	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv834166	chr22:27628570-27814359	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv834167	chr22:27758395-27910985	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv459864	chr22:27760086-27865344	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv588875	chr22:27760086-27865344	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7291247	C22orf31	cis	parietal	SCAN
rs7291247	EMID1	cis	cerebellum	SCAN
rs7291247	SUSD2	cis	cerebellum	SCAN
rs7291247	ST6GALNAC3	trans	cerebellum	SCAN
rs7291247	BCR	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27803000-27811600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:27804000-27812000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr22:27804200-27810800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr22:27804400-27810400	Weak transcription	Brain Germinal Matrix	brain
5	chr22:27806800-27811800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr22:27807200-27811600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr22:27808200-27810000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:27808400-27810000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr22:27809000-27809600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr22:27809000-27809800	Enhancers	HMEC	breast
11	chr22:27809000-27812000	Weak transcription	Spleen	Spleen
12	chr22:27809200-27809600	Flanking Active TSS	NHEK	skin
13	chr22:27809200-27809800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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