Variant report

Variant	rs9536266
Chromosome Location	chr13:53313657-53313658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr13:53312917-53314289	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr13:53313520-53313670	HVMF	connective:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
3	CTCF	chr13:53313540-53313690	HUVEC	blood vessel:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
4	CTCF	chr13:53313520-53313670	GM12874	blood:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
5	CTBP2	chr13:53312706-53314449	H1-hESC	embryonic stem cell:	n/a	n/a
6	CREB1	chr13:53313579-53314229	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr13:53313520-53313670	GM12872	blood:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
8	E2F6	chr13:53312650-53314281	H1-hESC	embryonic stem cell:	n/a	chr13:53314011-53314023 chr13:53313144-53313153
9	POLR2A	chr13:53313624-53313980	GM12878	blood:	n/a	n/a
10	CTCF	chr13:53312910-53313709	GM12878	blood:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
11	CTCF	chr13:53313620-53313770	HA-sp	spinal cord:	n/a	n/a
12	CTCF	chr13:53313418-53313702	GM12891	blood:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
13	CTCF	chr13:53313540-53313690	HRE	kidney:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
14	CTCF	chr13:53313453-53313697	GM19238	blood:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
15	CHD2	chr13:53313642-53313822	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr13:53312731-53314125	H1-hESC	embryonic stem cell:	n/a	chr13:53313612-53313621
17	CTCF	chr13:53313540-53313690	HRPEpiC	eye:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
18	CTCF	chr13:53313560-53313710	WI-38	lung:	n/a	chr13:53313573-53313586
19	CTCF	chr13:53313466-53313675	GM19239	blood:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
20	HDAC2	chr13:53312602-53313957	H1-hESC	embryonic stem cell:	n/a	n/a
21	ELF1	chr13:53313317-53313777	GM12878	blood:	n/a	n/a
22	CTCF	chr13:53313477-53313688	H1-hESC	embryonic stem cell:	n/a	chr13:53313540-53313558 chr13:53313541-53313557 chr13:53313542-53313555 chr13:53313573-53313586
23	BACH1	chr13:53312164-53313996	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr13:53312720-53314324	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
LECT1	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs12146944	1.00[ASN][1000 genomes]
rs1370082	0.80[AMR][1000 genomes]
rs1436724	0.80[AMR][1000 genomes]
rs1436725	0.80[AMR][1000 genomes]
rs2033680	1.00[AMR][1000 genomes]
rs2033684	0.80[AMR][1000 genomes]
rs2033685	0.80[AMR][1000 genomes]
rs2099547	0.83[AMR][1000 genomes]
rs2408659	1.00[AMR][1000 genomes]
rs3989920	0.91[AMR][1000 genomes]
rs4261419	0.80[AMR][1000 genomes]
rs4278636	0.80[AMR][1000 genomes]
rs4539485	0.80[AMR][1000 genomes]
rs4884223	0.80[AMR][1000 genomes]
rs4884240	0.80[AMR][1000 genomes]
rs4885887	0.80[AMR][1000 genomes]
rs4885910	0.80[AMR][1000 genomes]
rs61311520	0.83[AMR][1000 genomes]
rs61958127	0.82[EUR][1000 genomes]
rs61958693	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958694	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959591	0.83[AFR][1000 genomes]
rs61959592	0.83[AFR][1000 genomes]
rs61959594	0.83[AFR][1000 genomes]
rs61959595	0.83[AFR][1000 genomes]
rs61959616	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61959617	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61959618	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61959619	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61959620	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs61959653	0.91[AMR][1000 genomes]
rs61959654	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61959656	0.83[AMR][1000 genomes]
rs61961160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61961162	1.00[ASN][1000 genomes]
rs61961163	1.00[ASN][1000 genomes]
rs6561679	0.80[AMR][1000 genomes]
rs6561685	1.00[AMR][1000 genomes]
rs6561686	1.00[AMR][1000 genomes]
rs7325840	0.80[AMR][1000 genomes]
rs7330193	0.80[AMR][1000 genomes]
rs7330361	0.80[AMR][1000 genomes]
rs7330755	0.80[AMR][1000 genomes]
rs7986540	0.80[AMR][1000 genomes]
rs7992165	0.80[AMR][1000 genomes]
rs7994651	0.80[AMR][1000 genomes]
rs7996692	0.80[AMR][1000 genomes]
rs7999466	0.80[AMR][1000 genomes]
rs9316581	0.80[AMR][1000 genomes]
rs9316582	0.80[AMR][1000 genomes]
rs9316583	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9526964	0.83[AFR][1000 genomes]
rs9526966	0.83[AFR][1000 genomes]
rs9526972	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9526973	0.80[AMR][1000 genomes]
rs9526976	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9526978	0.80[AMR][1000 genomes]
rs9526986	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9526987	0.83[AMR][1000 genomes]
rs9526988	1.00[AMR][1000 genomes]
rs9526993	0.83[AMR][1000 genomes]
rs9526997	0.83[AMR][1000 genomes]
rs9536228	0.80[AMR][1000 genomes]
rs9536229	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9536232	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9536233	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9536235	0.80[AMR][1000 genomes]
rs9536237	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9536238	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9536240	0.80[AMR][1000 genomes]
rs9536241	0.80[AMR][1000 genomes]
rs9536243	0.80[AMR][1000 genomes]
rs9536244	0.80[AMR][1000 genomes]
rs9536246	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9536248	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9536249	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9536250	1.00[AMR][1000 genomes]
rs9536255	1.00[AMR][1000 genomes]
rs9536256	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9536257	0.83[AMR][1000 genomes]
rs9536260	1.00[AMR][1000 genomes]
rs9536261	1.00[AMR][1000 genomes]
rs9536264	0.83[AMR][1000 genomes]
rs9568752	0.80[AMR][1000 genomes]
rs9596671	0.80[AMR][1000 genomes]
rs971513	0.80[AMR][1000 genomes]
rs973198	0.80[AMR][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	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
2	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
3	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9536266	CKAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53312400-53314000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr13:53312600-53313800	Bivalent Enhancer	Liver	Liver
3	chr13:53312600-53314000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr13:53312800-53313800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr13:53312800-53313800	Bivalent Enhancer	Primary B cells from cord blood	blood
6	chr13:53312800-53313800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr13:53312800-53313800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:53312800-53313800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
9	chr13:53312800-53313800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
10	chr13:53312800-53313800	Bivalent Enhancer	Stomach Mucosa	stomach
11	chr13:53312800-53314000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:53312800-53314000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr13:53312800-53314000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
14	chr13:53312800-53314000	Enhancers	Gastric	stomach
15	chr13:53313000-53313800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
16	chr13:53313000-53313800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
17	chr13:53313000-53313800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
18	chr13:53313000-53313800	Bivalent/Poised TSS	Thymus	Thymus
19	chr13:53313000-53313800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
20	chr13:53313000-53314000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr13:53313000-53314000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr13:53313000-53314000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
23	chr13:53313000-53314200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr13:53313000-53314200	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr13:53313000-53314200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr13:53313000-53314400	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr13:53313000-53314400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr13:53313000-53314600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr13:53313000-53314800	Bivalent Enhancer	Fetal Brain Male	brain
30	chr13:53313200-53313800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:53313200-53313800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
32	chr13:53313200-53313800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
33	chr13:53313200-53313800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
34	chr13:53313200-53313800	Enhancers	Lung	lung
35	chr13:53313200-53314000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr13:53313200-53314000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:53313200-53314000	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr13:53313200-53314000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:53313200-53314000	Bivalent Enhancer	Fetal Thymus	thymus
40	chr13:53313200-53314400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr13:53313400-53313800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr13:53313400-53313800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr13:53313400-53313800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr13:53313400-53313800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
45	chr13:53313400-53313800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
46	chr13:53313400-53313800	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr13:53313400-53313800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
48	chr13:53313400-53313800	Bivalent/Poised TSS	HepG2	liver
49	chr13:53313400-53313800	Bivalent Enhancer	NH-A	brain
50	chr13:53313400-53314000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain

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