Variant report

Variant	rs9568366
Chromosome Location	chr13:50566466-50566467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50564697..50567358-chr13:50569742..50572232,5	MCF-7	breast:
2	chr13:50564025..50567243-chr13:51483515..51485383,3	K562	blood:

Variant related genes	Relation type
ENSG00000264864	Chromatin interaction
ENSG00000136104	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000233672	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11617754	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs2066549	0.90[CHB][hapmap]
rs2066557	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs2066571	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2066575	0.90[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs2066585	0.90[CHB][hapmap]
rs2066591	0.90[CHB][hapmap]
rs2242482	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs2472599	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2475837	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2687950	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs2687951	0.90[CHB][hapmap]
rs2740524	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2740544	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs2740545	0.90[CHB][hapmap]
rs2760914	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs2803839	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs2812222	0.90[CHB][hapmap]
rs28798976	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3116591	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4548769	0.90[CHB][hapmap]
rs4942899	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs4942903	0.82[CHB][hapmap]
rs706610	0.81[CHB][hapmap]
rs73489861	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73489862	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs790943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7986337	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs809845	0.81[CHB][hapmap]
rs9535407	0.90[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs9562941	0.81[CHB][hapmap]
rs9568348	0.80[CHB][hapmap]
rs9568354	0.84[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs9568357	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs9568359	0.81[CHB][hapmap]
rs9596219	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs9596220	0.90[CHB][hapmap];0.82[CHD][hapmap];0.81[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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9568366	KCTD4	cis	parietal	SCAN
rs9568366	SNORA2B	trans	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50539000-50570000	Weak transcription	Fetal Intestine Small	intestine
2	chr13:50540400-50569800	Weak transcription	Primary T cells from cord blood	blood
3	chr13:50543600-50570400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:50546000-50569200	Weak transcription	Primary B cells from cord blood	blood
5	chr13:50546000-50570000	Weak transcription	NHLF	lung
6	chr13:50547600-50569800	Weak transcription	Dnd41	blood
7	chr13:50550800-50569600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr13:50550800-50569800	Weak transcription	NH-A	brain
9	chr13:50551000-50569600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr13:50551000-50569600	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:50551000-50569800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr13:50551000-50569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:50551000-50569800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr13:50551000-50570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr13:50551000-50570200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr13:50551200-50569600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr13:50551400-50570200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:50552400-50568800	Weak transcription	GM12878-XiMat	blood
19	chr13:50552400-50570200	Weak transcription	Lung	lung
20	chr13:50552800-50569800	Weak transcription	Fetal Lung	lung
21	chr13:50552800-50569800	Weak transcription	Placenta	Placenta
22	chr13:50552800-50570200	Weak transcription	Spleen	Spleen
23	chr13:50553600-50570000	Weak transcription	Left Ventricle	heart
24	chr13:50555000-50569200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr13:50555200-50569600	Weak transcription	Fetal Stomach	stomach
26	chr13:50555200-50569800	Weak transcription	Brain Angular Gyrus	brain
27	chr13:50556000-50568200	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr13:50556800-50570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr13:50557000-50569800	Weak transcription	Fetal Brain Female	brain
30	chr13:50557200-50570000	Weak transcription	Aorta	Aorta
31	chr13:50557600-50568600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr13:50558000-50569600	Weak transcription	HUVEC	blood vessel
33	chr13:50558200-50570000	Weak transcription	Esophagus	oesophagus
34	chr13:50558600-50566800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr13:50558600-50569800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr13:50558600-50569800	Weak transcription	HSMMtube	muscle
37	chr13:50558800-50567200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr13:50559800-50569800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr13:50560000-50569600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr13:50560000-50570000	Weak transcription	Pancreas	Pancrea
41	chr13:50560200-50569800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr13:50560200-50569800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr13:50560400-50569800	Weak transcription	Brain Anterior Caudate	brain
44	chr13:50560800-50566800	Strong transcription	Osteobl	bone
45	chr13:50561000-50568600	Strong transcription	Fetal Thymus	thymus
46	chr13:50561200-50569800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr13:50561200-50570000	Weak transcription	Psoas Muscle	Psoas
48	chr13:50561400-50569800	Weak transcription	Fetal Heart	heart
49	chr13:50562200-50569800	Weak transcription	Brain Substantia Nigra	brain
50	chr13:50562200-50569800	Weak transcription	Fetal Kidney	kidney

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