Variant report

Variant	rs10800393
Chromosome Location	chr1:168862571-168862572
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr1:168862553-168862841	MCF10A-Er-Src	breast:	n/a	chr1:168862757-168862769

Variant related genes	Relation type
SUMO1P2	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10489364	0.95[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10753780	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10753781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800390	0.87[ASN][1000 genomes]
rs10800391	0.87[ASN][1000 genomes]
rs10800392	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919006	0.98[ASN][1000 genomes]
rs10919011	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1322498	0.87[ASN][1000 genomes]
rs1322499	0.80[ASN][1000 genomes]
rs1407477	0.83[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1570335	0.83[CHB][hapmap];0.89[TSI][hapmap]
rs1575329	0.85[ASN][1000 genomes]
rs1590285	0.88[ASN][1000 genomes]
rs1885557	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2065129	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34298853	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36197047	0.81[ASN][1000 genomes]
rs4142003	0.81[EUR][1000 genomes]
rs4656162	0.85[ASN][1000 genomes]
rs4656163	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656622	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656624	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6427155	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657987	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6666564	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6670083	0.83[CHB][hapmap];0.89[TSI][hapmap]
rs6683127	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6683236	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6683991	0.85[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6694810	0.85[ASN][1000 genomes]
rs6702913	0.85[ASN][1000 genomes]
rs715008	0.82[ASN][1000 genomes]
rs7514435	0.83[CHB][hapmap];0.89[TSI][hapmap]
rs7525262	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7544924	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7550083	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs857633	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs857635	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	nsv437258	chr1:168824111-168890420	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10800393	POGK	cis	cerebellum	SCAN
rs10800393	MAEL	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168861800-168865200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:168862000-168862600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:168862000-168862800	Enhancers	Brain Angular Gyrus	brain
4	chr1:168862000-168863000	Enhancers	Colon Smooth Muscle	Colon
5	chr1:168862000-168863200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:168862000-168863200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:168862000-168863200	Enhancers	Fetal Stomach	stomach
8	chr1:168862000-168863200	Enhancers	Ovary	ovary
9	chr1:168862000-168863200	Enhancers	Stomach Smooth Muscle	stomach
10	chr1:168862000-168863200	Enhancers	HMEC	breast
11	chr1:168862000-168863200	Enhancers	HSMM	muscle
12	chr1:168862000-168863200	Enhancers	HSMMtube	muscle
13	chr1:168862000-168865000	Enhancers	Fetal Lung	lung
14	chr1:168862200-168862600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:168862200-168862600	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:168862200-168862800	Enhancers	Brain Anterior Caudate	brain
17	chr1:168862200-168863000	Enhancers	Brain Hippocampus Middle	brain
18	chr1:168862200-168863000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr1:168862200-168863200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:168862200-168863200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr1:168862400-168862600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr1:168862400-168862600	Flanking Active TSS	NHEK	skin
23	chr1:168862400-168863000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:168862400-168863000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr1:168862400-168863200	Enhancers	Rectal Smooth Muscle	rectum
26	chr1:168862400-168863200	Enhancers	NHDF-Ad	bronchial
27	chr1:168862400-168877000	Weak transcription	Fetal Heart	heart

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