Variant report

Variant	rs159762
Chromosome Location	chr4:124322594-124322595
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	chr4:124321330..124323743-chr4:124325294..124328181,3	K562	blood:
2	chr4:124317259..124319394-chr4:124319799..124323152,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164056	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs167297	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28672261	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300562	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300563	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300564	1.00[CEU][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300569	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407317	0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs442351	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4833913	1.00[ASN][1000 genomes]
rs623936	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006945	chr4:124206328-124503863	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv537240	chr4:124206328-124503863	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs159762	KIAA1109	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124317200-124323000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:124317400-124322600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr4:124317400-124322600	Active TSS	Colon Smooth Muscle	Colon
4	chr4:124317400-124322600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr4:124317400-124322600	Active TSS	Psoas Muscle	Psoas
6	chr4:124317400-124322800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:124317400-124322800	Active TSS	Aorta	Aorta
8	chr4:124317400-124322800	Active TSS	Rectal Mucosa Donor 31	rectum
9	chr4:124317400-124322800	Active TSS	NHLF	lung
10	chr4:124317400-124323200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:124317400-124327000	Active TSS	Right Atrium	heart
12	chr4:124317600-124322600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr4:124317600-124322600	Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr4:124317600-124322600	Active TSS	Brain Hippocampus Middle	brain
15	chr4:124317600-124322600	Active TSS	Left Ventricle	heart
16	chr4:124317600-124322600	Active TSS	Thymus	Thymus
17	chr4:124317600-124322800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:124317600-124322800	Active TSS	Duodenum Mucosa	Duodenum
19	chr4:124317600-124322800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr4:124317600-124322800	Active TSS	Rectal Smooth Muscle	rectum
21	chr4:124317600-124323000	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr4:124318800-124324600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:124318800-124327000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:124320000-124322800	Active TSS	Right Ventricle	heart
25	chr4:124320200-124322800	Active TSS	Fetal Stomach	stomach
26	chr4:124320200-124324600	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
27	chr4:124320400-124322800	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr4:124320800-124322800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:124320800-124322800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:124321000-124322800	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr4:124321000-124323000	Weak transcription	Spleen	Spleen
32	chr4:124321000-124324000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr4:124321200-124322600	Weak transcription	Gastric	stomach
34	chr4:124321200-124322800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:124321200-124322800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:124321200-124323200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:124321200-124324600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
38	chr4:124321400-124322600	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr4:124321400-124322800	Weak transcription	Esophagus	oesophagus
40	chr4:124321400-124323000	Weak transcription	Pancreas	Pancrea
41	chr4:124321400-124323000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr4:124321400-124323200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
43	chr4:124321400-124337200	Weak transcription	A549	lung
44	chr4:124321600-124322800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:124321600-124323000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr4:124321600-124323000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr4:124321600-124323000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:124321600-124323200	Weak transcription	Placenta	Placenta
49	chr4:124321600-124323800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr4:124321600-124326400	Weak transcription	Liver	Liver

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