Variant report

Variant	rs9535829
Chromosome Location	chr13:52576073-52576074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52025684..52028500-chr13:52574540..52576324,2	K562	blood:
2	chr13:52573978..52576897-chr13:52584867..52586656,2	MCF-7	breast:
3	chr13:52571069..52573595-chr13:52575661..52577767,2	K562	blood:

Variant related genes	Relation type
ENSG00000253710	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000123191	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11616964	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11620583	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12584961	0.83[EUR][1000 genomes]
rs1801243	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1801244	0.82[AMR][1000 genomes]
rs1886542	0.84[ASN][1000 genomes]
rs1886547	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1924611	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1951922	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1998696	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2004866	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2181891	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2274202	0.83[ASN][1000 genomes]
rs2296348	0.84[ASN][1000 genomes]
rs2296349	0.84[ASN][1000 genomes]
rs2296350	0.84[ASN][1000 genomes]
rs2408544	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2408549	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2408550	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2408551	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2408609	0.83[ASN][1000 genomes]
rs2408611	0.84[ASN][1000 genomes]
rs28393037	0.83[ASN][1000 genomes]
rs2897976	0.83[ASN][1000 genomes]
rs2897977	0.84[ASN][1000 genomes]
rs3368	0.84[ASN][1000 genomes]
rs35895576	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742288	0.82[AMR][1000 genomes]
rs3825527	0.82[AMR][1000 genomes]
rs3825528	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4297592	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55772266	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61958812	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6650383	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs723102	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs723103	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7327634	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7337430	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs750290	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs755363	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7993492	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7994928	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7995946	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7999812	0.82[AMR][1000 genomes]
rs9316563	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526819	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526821	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526832	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9526837	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9526842	0.82[ASN][1000 genomes]
rs9535812	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9535817	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535819	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535822	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535823	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535826	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535828	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535830	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535832	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535833	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535836	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535849	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535851	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535858	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535860	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535862	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535866	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535872	0.85[ASN][1000 genomes]
rs9535878	0.83[ASN][1000 genomes]
rs9535879	0.84[ASN][1000 genomes]
rs9535880	0.84[ASN][1000 genomes]
rs9535885	0.81[ASN][1000 genomes]
rs9535887	0.82[ASN][1000 genomes]
rs9563084	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9563089	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9563091	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9563093	0.82[ASN][1000 genomes]
rs9568681	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9568693	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568695	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568708	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568713	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv1041996	chr13:52544805-52581501	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
6	esv2763022	chr13:52544978-52581513	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
7	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
9	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9535829	ALG11	cis	Muscle Skeletal	GTEx
rs9535829	NEK3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52570800-52577600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr13:52570800-52585000	Weak transcription	Colonic Mucosa	Colon
3	chr13:52570800-52585200	Weak transcription	Aorta	Aorta
4	chr13:52571000-52583800	Weak transcription	Brain Germinal Matrix	brain
5	chr13:52573200-52578400	Weak transcription	Gastric	stomach
6	chr13:52574000-52576200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr13:52574000-52577000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:52574000-52577000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr13:52574000-52584400	Weak transcription	Fetal Stomach	stomach
10	chr13:52574200-52577800	Weak transcription	Pancreas	Pancrea
11	chr13:52574200-52578800	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:52574200-52579000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:52574200-52584400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr13:52574200-52585000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:52574400-52576400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr13:52574400-52577600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr13:52574400-52579800	Weak transcription	Placenta	Placenta
18	chr13:52574400-52584400	Weak transcription	Psoas Muscle	Psoas
19	chr13:52574400-52584400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr13:52574400-52585000	Weak transcription	Left Ventricle	heart
21	chr13:52574400-52585200	Weak transcription	Lung	lung
22	chr13:52574600-52576400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr13:52574600-52578800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr13:52574600-52584400	Weak transcription	Fetal Brain Female	brain
25	chr13:52574800-52578400	Weak transcription	Brain Angular Gyrus	brain
26	chr13:52574800-52578800	Enhancers	HepG2	liver
27	chr13:52575000-52577200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr13:52575000-52577200	Weak transcription	Fetal Muscle Leg	muscle
29	chr13:52575400-52578600	Weak transcription	Liver	Liver
30	chr13:52575400-52580200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:52575400-52580400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr13:52575600-52576400	Weak transcription	Stomach Mucosa	stomach
33	chr13:52575600-52576800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr13:52575800-52576400	Weak transcription	Fetal Intestine Small	intestine
35	chr13:52575800-52576800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr13:52575800-52576800	Weak transcription	Fetal Intestine Large	intestine
37	chr13:52575800-52578600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr13:52575800-52581800	Weak transcription	K562	blood
39	chr13:52576000-52576200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr13:52576000-52576600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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