Variant report

Variant	rs12463552
Chromosome Location	chr2:31451224-31451225
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10204574	0.91[JPT][hapmap]
rs13393359	0.90[JPT][hapmap]
rs2044243	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2344	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs602614	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6722609	0.82[ASN][1000 genomes]
rs6750820	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6753831	0.86[JPT][hapmap]
rs754731	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs754732	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs754733	0.83[ASN][1000 genomes]
rs7595906	0.93[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv430635	chr2:31420415-31464385	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1009712	chr2:31424588-31468364	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1000416	chr2:31424588-31470845	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv581268	chr2:31425783-31467079	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1001299	chr2:31428030-31464385	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv430646	chr2:31428030-31464385	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12463552	TTC27	cis	parietal	SCAN
rs12463552	EHD3	cis	parietal	SCAN
rs12463552	FAM98A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31445000-31453800	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr2:31446200-31456200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:31446400-31455800	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:31448800-31456600	Weak transcription	Spleen	Spleen
5	chr2:31449600-31456000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:31449800-31455600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:31450400-31451400	Enhancers	Fetal Heart	heart
8	chr2:31451000-31451400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:31451000-31455600	Weak transcription	Esophagus	oesophagus
10	chr2:31451000-31455800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:31451000-31456000	Weak transcription	Left Ventricle	heart
12	chr2:31451200-31451400	Enhancers	NHEK	skin
13	chr2:31451200-31455200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:31451200-31456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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