Variant report

Variant	rs11189376
Chromosome Location	chr10:99546400-99546401
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10748709	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10786367	0.81[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs10786371	0.91[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10786372	0.90[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10786373	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10786374	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10882995	0.91[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs10882996	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10882997	0.82[ASN][1000 genomes]
rs10882998	0.94[CEU][hapmap]
rs11189350	0.83[ASN][1000 genomes]
rs11189352	0.83[ASN][1000 genomes]
rs11189353	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11189355	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11189356	0.86[ASN][1000 genomes]
rs11189357	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs11189359	0.91[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs11189360	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11189361	0.81[ASN][1000 genomes]
rs11189362	0.85[JPT][hapmap]
rs11189367	0.94[ASN][1000 genomes]
rs11189374	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189377	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11591898	0.86[ASN][1000 genomes]
rs11597378	0.94[CHB][hapmap]
rs12412543	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12569711	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12569757	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12780534	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12783992	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1538723	0.87[ASN][1000 genomes]
rs1981237	0.82[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs1981238	0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2010732	0.83[EUR][1000 genomes]
rs2039826	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34283185	0.82[ASN][1000 genomes]
rs3750614	0.91[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs3750615	0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3814558	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3814559	0.86[JPT][hapmap]
rs3814560	0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs4244329	0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs4244330	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4917784	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4917785	0.80[ASN][1000 genomes]
rs4917786	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4919139	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7072751	0.82[ASN][1000 genomes]
rs7080894	0.86[JPT][hapmap]
rs7080953	0.85[JPT][hapmap]
rs7081361	0.82[ASN][1000 genomes]
rs7081652	0.81[EUR][1000 genomes]
rs7094519	0.85[EUR][1000 genomes]
rs7099540	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7100453	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7478323	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7910589	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7916454	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs7922907	0.85[JPT][hapmap]
rs946777	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs946778	0.91[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11189376	ZFYVE27	cis	cerebellum	SCAN
rs11189376	DHDPSL	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99541000-99548600	Weak transcription	A549	lung
2	chr10:99541400-99546400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr10:99541800-99548400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:99541800-99548600	Weak transcription	Right Atrium	heart
5	chr10:99541800-99548800	Weak transcription	Right Ventricle	heart
6	chr10:99542600-99546400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:99542600-99548400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr10:99542800-99547800	Weak transcription	Stomach Mucosa	stomach
9	chr10:99542800-99548400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr10:99542800-99548600	Weak transcription	Fetal Lung	lung
11	chr10:99543000-99547600	Weak transcription	K562	blood
12	chr10:99543000-99548400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr10:99543000-99551400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr10:99543200-99548400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr10:99543200-99548400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr10:99543200-99548400	Weak transcription	Left Ventricle	heart
17	chr10:99543200-99551400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr10:99543800-99547200	Enhancers	Fetal Intestine Large	intestine
19	chr10:99544000-99548400	Weak transcription	Brain Substantia Nigra	brain
20	chr10:99544000-99548600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr10:99544600-99550800	Weak transcription	Gastric	stomach
22	chr10:99545000-99546400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:99545600-99547600	Flanking Active TSS	Pancreas	Pancrea
24	chr10:99545800-99547000	Bivalent Enhancer	HepG2	liver
25	chr10:99546000-99546400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr10:99546000-99546400	Enhancers	NHEK	skin
27	chr10:99546000-99546600	Enhancers	Lung	lung
28	chr10:99546000-99546800	Flanking Active TSS	Fetal Intestine Small	intestine
29	chr10:99546200-99546800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr10:99546400-99546600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr10:99546400-99546600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:99546400-99548400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr10:99546400-99548400	Weak transcription	NHEK	skin
34	chr10:99546400-99548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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