Variant report

Variant	rs10776658
Chromosome Location	chr10:50143591-50143592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1015717	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10745290	0.85[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs10776659	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10776660	0.85[CEU][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs10857430	0.85[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs10857661	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857662	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11101572	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11101573	0.92[CEU][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs12413832	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1877799	0.85[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs1913516	0.84[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs2137909	0.85[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs2137913	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2249662	0.92[JPT][hapmap]
rs2255553	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2271565	0.85[CEU][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs2292584	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2292585	0.85[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2457466	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2663028	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2663067	0.88[CEU][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs2663068	0.97[CHD][hapmap]
rs2671715	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2889709	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs3750867	0.94[EUR][1000 genomes]
rs3829206	0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4317902	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4614357	0.84[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4838663	0.85[EUR][1000 genomes]
rs61848117	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6537586	0.85[CEU][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs6537587	0.85[CEU][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7072344	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7082322	0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7083751	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs7086917	0.89[CEU][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7091429	0.85[CEU][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs7093656	0.85[CEU][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs7098224	0.92[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831865	chr10:49994254-50164239	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10776658	CSTF2T	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50121000-50155800	Weak transcription	Primary T cells from cord blood	blood
2	chr10:50125400-50154400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr10:50127800-50147000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr10:50127800-50150400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr10:50127800-50150600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:50130800-50143600	Strong transcription	Primary B cells from cord blood	blood
7	chr10:50134600-50160400	Weak transcription	Right Atrium	heart
8	chr10:50135400-50149800	Weak transcription	Spleen	Spleen
9	chr10:50135600-50145800	Weak transcription	GM12878-XiMat	blood
10	chr10:50138600-50145400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:50139800-50143600	Weak transcription	Pancreas	Pancrea
12	chr10:50142000-50146400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr10:50142600-50143600	Flanking Active TSS	Fetal Lung	lung
14	chr10:50142600-50145800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr10:50142600-50148000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr10:50142800-50143600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr10:50142800-50143600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:50142800-50143600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr10:50143000-50143600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr10:50143000-50143600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr10:50143000-50143600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr10:50143000-50143600	Active TSS	Brain Anterior Caudate	brain
23	chr10:50143000-50145000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr10:50143200-50143600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr10:50143200-50143600	Flanking Active TSS	Brain Germinal Matrix	brain
26	chr10:50143200-50143800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:50143200-50143800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr10:50143200-50144000	Flanking Active TSS	Dnd41	blood
29	chr10:50143400-50143600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:50143400-50143600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:50143400-50143600	Enhancers	Fetal Stomach	stomach
32	chr10:50143400-50148800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr10:50143400-50153200	Weak transcription	Fetal Muscle Leg	muscle

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