Variant report

Variant	rs11792628
Chromosome Location	chr9:116010472-116010473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10123415	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10125992	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10513189	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739388	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10739390	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10739392	0.86[EUR][1000 genomes]
rs10759633	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10759636	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759637	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10817461	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10817468	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4129395	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4129396	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4129397	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4284098	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4560868	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4979223	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4979226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6477998	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6477999	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7022397	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7038769	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7041615	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850357	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7851395	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7859354	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv893746	chr9:115983540-116022826	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11792628	CDC26	cis	Esophagus Muscularis	GTEx
rs11792628	CDC26	cis	Heart Left Ventricle	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115985000-116020800	Weak transcription	Aorta	Aorta
2	chr9:115985600-116020800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:115985800-116018400	Weak transcription	NHEK	skin
4	chr9:115985800-116019000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:115985800-116021000	Weak transcription	Fetal Stomach	stomach
6	chr9:115986400-116013000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:115987600-116017800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:115987600-116018200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:115987800-116011000	Weak transcription	A549	lung
10	chr9:115987800-116021000	Weak transcription	Hela-S3	cervix
11	chr9:115989000-116019200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:115991000-116011600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:115995200-116017800	Weak transcription	Left Ventricle	heart
14	chr9:115995400-116018000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:115996000-116022200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr9:115996000-116031600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:115996200-116018600	Weak transcription	Primary T cells from cord blood	blood
18	chr9:115996200-116022400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr9:115996600-116019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:115998400-116018200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:115998600-116013000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:116000000-116017400	Weak transcription	HepG2	liver
23	chr9:116002000-116018400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:116002200-116018400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:116004400-116020400	Weak transcription	Fetal Thymus	thymus
26	chr9:116004800-116013000	Weak transcription	Liver	Liver
27	chr9:116005200-116017600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:116005800-116011600	Weak transcription	Fetal Intestine Small	intestine
29	chr9:116006000-116018000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:116006000-116018400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:116006200-116020400	Weak transcription	Psoas Muscle	Psoas
32	chr9:116007200-116019200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:116007200-116019400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr9:116007200-116020800	Weak transcription	Ovary	ovary
35	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr9:116009600-116013000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr9:116009600-116019000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:116009600-116020200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:116009600-116029800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr9:116009800-116013000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr9:116010000-116018000	Weak transcription	K562	blood
42	chr9:116010000-116020000	Weak transcription	GM12878-XiMat	blood
43	chr9:116010200-116031800	Weak transcription	Fetal Heart	heart

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