Variant report

Variant	rs10798780
Chromosome Location	chr1:180546296-180546297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10494530	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs10737347	0.81[ASN][1000 genomes]
rs10737348	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs10798781	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845403	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs3845404	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs3856052	0.81[ASN][1000 genomes]
rs3856055	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs4111062	0.84[ASN][1000 genomes]
rs4111063	0.81[ASN][1000 genomes]
rs4111064	0.81[ASN][1000 genomes]
rs4144583	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs7519155	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7521872	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs7544326	0.84[ASN][1000 genomes]
rs7551817	0.80[ASN][1000 genomes]
rs7554099	0.91[CHB][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10798780	C1orf220	cis	parietal	SCAN
rs10798780	SOAT1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180541600-180549600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:180543200-180547400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr1:180543400-180546400	Weak transcription	Pancreas	Pancrea
4	chr1:180543800-180548800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:180544000-180549000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:180544000-180549000	Weak transcription	Stomach Mucosa	stomach
7	chr1:180544200-180548800	Weak transcription	HMEC	breast
8	chr1:180544400-180548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:180545000-180546600	Weak transcription	Fetal Brain Male	brain
10	chr1:180545200-180549000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:180545200-180549400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:180545200-180549400	Weak transcription	K562	blood
13	chr1:180545200-180549400	Weak transcription	NHEK	skin
14	chr1:180545800-180549200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:180546000-180547200	Enhancers	Osteobl	bone
16	chr1:180546200-180546400	Enhancers	Left Ventricle	heart
17	chr1:180546200-180546800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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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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