Variant report

Variant	rs300574
Chromosome Location	chr4:124323738-124323739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:124323722..124325703-chr4:124328935..124331134,3	K562	blood:
2	chr4:124318413..124320178-chr4:124322653..124324749,2	MCF-7	breast:
3	chr4:124321330..124323743-chr4:124325294..124328181,3	K562	blood:

Variant related genes	Relation type
ENSG00000164056	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10518414	0.91[ASN][1000 genomes]
rs11098709	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13145927	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13150612	0.97[ASN][1000 genomes]
rs188513	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28477228	0.98[ASN][1000 genomes]
rs28514996	0.97[ASN][1000 genomes]
rs300555	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs300572	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs300573	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4833277	0.98[ASN][1000 genomes]
rs4833278	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs9992811	0.97[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
rs300574	KIAA1109	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124317400-124327000	Active TSS	Right Atrium	heart
2	chr4:124318800-124324600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:124318800-124327000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:124320200-124324600	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
5	chr4:124321000-124324000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:124321200-124324600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
7	chr4:124321400-124337200	Weak transcription	A549	lung
8	chr4:124321600-124323800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:124321600-124326400	Weak transcription	Liver	Liver
10	chr4:124321600-124328000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:124321600-124328000	Weak transcription	Small Intestine	intestine
12	chr4:124321800-124324200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:124321800-124337400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr4:124322000-124324400	Weak transcription	NH-A	brain
15	chr4:124322000-124325800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:124322000-124327600	Weak transcription	Fetal Brain Female	brain
17	chr4:124322200-124324600	Transcr. at gene 5' and 3'	Fetal Lung	lung
18	chr4:124322200-124325400	Transcr. at gene 5' and 3'	HepG2	liver
19	chr4:124322400-124324000	Genic enhancers	Fetal Thymus	thymus
20	chr4:124322400-124324600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:124322400-124324600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
22	chr4:124322400-124325000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
23	chr4:124322400-124334000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:124322600-124324000	Transcr. at gene 5' and 3'	Left Ventricle	heart
25	chr4:124322600-124324600	Genic enhancers	H1 Cell Line	embryonic stem cell
26	chr4:124322600-124324600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
27	chr4:124322600-124324600	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
28	chr4:124322600-124326200	Weak transcription	Brain Hippocampus Middle	brain
29	chr4:124322600-124326600	Weak transcription	Fetal Heart	heart
30	chr4:124322800-124323800	Strong transcription	Primary T cells from cord blood	blood
31	chr4:124322800-124323800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:124322800-124323800	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
33	chr4:124322800-124324000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
34	chr4:124322800-124324000	Transcr. at gene 5' and 3'	NHLF	lung
35	chr4:124322800-124324200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:124322800-124324400	Transcr. at gene 5' and 3'	Right Ventricle	heart
37	chr4:124322800-124324600	Strong transcription	Primary B cells from cord blood	blood
38	chr4:124322800-124324600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr4:124322800-124324600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:124322800-124324600	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
41	chr4:124322800-124324600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
42	chr4:124322800-124324800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
43	chr4:124322800-124325200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
44	chr4:124322800-124325400	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:124322800-124326400	Weak transcription	Fetal Brain Male	brain
46	chr4:124322800-124339000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:124323000-124323800	Genic enhancers	Brain Anterior Caudate	brain
48	chr4:124323000-124323800	Genic enhancers	Pancreas	Pancrea
49	chr4:124323000-124324000	Genic enhancers	H9 Cell Line	embryonic stem cell
50	chr4:124323000-124324000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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