Variant report

Variant	rs10793566
Chromosome Location	chr10:45411165-45411166
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10793567	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10793568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793569	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10900132	0.86[CHB][hapmap]
rs2065465	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs4396240	0.86[CHB][hapmap]
rs4948929	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948931	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6593449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6593450	0.96[ASN][1000 genomes]
rs7067692	0.86[CHB][hapmap]
rs7095112	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7100544	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7904676	0.81[JPT][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs7923073	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7923091	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs867317	0.91[ASN][1000 genomes]
rs914695	0.86[CHB][hapmap]
rs914696	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517161	chr10:45210690-45416256	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv831845	chr10:45300268-45460395	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv466909	chr10:45408011-45446791	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv550714	chr10:45408011-45446791	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2762860	chr10:45411165-45412956	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10793566	AGPHD1	trans	parietal	SCAN
rs10793566	RASGEF1A	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45401400-45415600	Weak transcription	Fetal Brain Female	brain
2	chr10:45406400-45419000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:45407200-45411600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr10:45407600-45411400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr10:45407800-45422800	Weak transcription	Ovary	ovary
6	chr10:45408600-45417200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:45409400-45411400	Enhancers	Fetal Thymus	thymus
8	chr10:45409600-45411200	Weak transcription	Fetal Kidney	kidney
9	chr10:45409600-45411800	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr10:45409600-45412800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr10:45409800-45412600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr10:45410000-45411400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr10:45410000-45412800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:45410000-45419000	Weak transcription	Pancreas	Pancrea
15	chr10:45410200-45411400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr10:45410200-45430400	Weak transcription	Gastric	stomach
17	chr10:45410400-45412400	Weak transcription	Fetal Heart	heart
18	chr10:45410600-45419600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr10:45411000-45413000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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

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