Variant report

Variant	rs10748709
Chromosome Location	chr10:99537490-99537491
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10786370	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10786371	0.82[JPT][hapmap]
rs10786373	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882993	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10882995	0.82[JPT][hapmap]
rs10882997	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882998	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11189353	0.81[JPT][hapmap]
rs11189357	0.81[JPT][hapmap]
rs11189359	0.83[JPT][hapmap]
rs11189360	0.80[JPT][hapmap]
rs11189361	0.85[ASN][1000 genomes]
rs11189362	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11189367	0.81[ASN][1000 genomes]
rs11189374	0.81[ASN][1000 genomes]
rs11189376	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11189377	0.82[ASN][1000 genomes]
rs11815012	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12268814	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12569757	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12783992	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1556971	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1981237	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1981238	0.85[JPT][hapmap]
rs2010732	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2027376	0.86[ASN][1000 genomes]
rs2039826	0.82[CHD][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2095957	0.85[EUR][1000 genomes]
rs34283185	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750612	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3750614	0.82[JPT][hapmap]
rs3750615	0.86[JPT][hapmap]
rs3814559	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3814560	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4244329	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4244330	0.80[ASN][1000 genomes]
rs4917786	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4919139	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7072751	0.99[ASN][1000 genomes]
rs7080894	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7080953	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7081652	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7094519	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7099540	0.82[JPT][hapmap]
rs7100453	0.81[ASN][1000 genomes]
rs7478323	0.80[ASN][1000 genomes]
rs7907679	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap]
rs7910589	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916164	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7916454	0.81[JPT][hapmap]
rs7916593	0.86[ASN][1000 genomes]
rs7922907	0.91[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs883324	0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs946777	0.81[JPT][hapmap]
rs946778	0.82[JPT][hapmap]

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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10748709	ZFYVE27	cis	cerebellum	SCAN
rs10748709	C10orf12	cis	cerebellum	SCAN
rs10748709	ZFYVE27	cis	parietal	SCAN
rs10748709	DHDPSL	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99532000-99540200	Weak transcription	Right Atrium	heart
2	chr10:99532800-99541000	Weak transcription	Gastric	stomach
3	chr10:99533600-99538200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:99533600-99541400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:99533800-99538200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:99536800-99537800	Enhancers	Duodenum Mucosa	Duodenum
7	chr10:99536800-99537800	Enhancers	Fetal Intestine Small	intestine
8	chr10:99536800-99537800	Enhancers	HepG2	liver
9	chr10:99537000-99537600	Enhancers	Fetal Intestine Large	intestine
10	chr10:99537000-99538800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:99537000-99545600	Enhancers	Pancreas	Pancrea
12	chr10:99537200-99538600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr10:99537200-99542600	Enhancers	Fetal Thymus	thymus

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