Variant report

Variant	rs9403540
Chromosome Location	chr6:144292587-144292588
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144291074..144293764-chr6:144327340..144330897,3	K562	blood:
2	chr6:144286109..144288326-chr6:144291907..144294386,3	K562	blood:
3	chr6:144285004..144287609-chr6:144292204..144295096,3	K562	blood:
4	chr6:144281173..144283834-chr6:144290896..144293315,2	K562	blood:

Variant related genes	Relation type
ENSG00000118495	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12175856	1.00[LWK][hapmap]
rs13218225	1.00[YRI][hapmap]
rs2092894	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[EUR][1000 genomes]
rs2224152	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2268448	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7770529	1.00[YRI][hapmap]
rs9321953	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9321956	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9373409	0.93[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs9376802	0.83[ASN][1000 genomes]
rs9386053	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390147	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9390148	1.00[CEU][hapmap];0.88[CHD][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs9390150	0.92[CEU][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9399468	1.00[CEU][hapmap];0.90[EUR][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	esv3408554	chr6:144106707-144369589	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3522138	chr6:144174685-144367463	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3522139	chr6:144174685-144367463	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830830	chr6:144177942-144380870	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9403540	PLAGL1	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144269600-144294000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr6:144269800-144296000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:144269800-144304400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:144271400-144296800	Weak transcription	Primary B cells from cord blood	blood
5	chr6:144275000-144293000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:144281800-144294800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:144284800-144294400	Weak transcription	Fetal Brain Male	brain
8	chr6:144284800-144318400	Weak transcription	Aorta	Aorta
9	chr6:144285400-144294200	Weak transcription	Left Ventricle	heart
10	chr6:144285800-144293400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr6:144286800-144294200	Weak transcription	Fetal Brain Female	brain
12	chr6:144287000-144293000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:144287000-144294400	Weak transcription	Lung	lung
14	chr6:144287000-144294800	Weak transcription	Spleen	Spleen
15	chr6:144287000-144298800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:144287200-144293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:144287200-144293200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:144287200-144293400	Weak transcription	Fetal Intestine Small	intestine
19	chr6:144287400-144294600	Enhancers	Adipose Nuclei	Adipose
20	chr6:144287600-144297600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:144287800-144292600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:144288200-144293400	Weak transcription	NHDF-Ad	bronchial
23	chr6:144288400-144314800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:144289000-144295000	Enhancers	Fetal Lung	lung
25	chr6:144289000-144301800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:144289200-144293400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:144289400-144294200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:144289800-144292800	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:144289800-144293200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:144290000-144294400	Weak transcription	Small Intestine	intestine
31	chr6:144290000-144296200	Weak transcription	NHLF	lung
32	chr6:144290200-144296000	Enhancers	Fetal Kidney	kidney
33	chr6:144290400-144294400	Weak transcription	Fetal Intestine Large	intestine
34	chr6:144290600-144294400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:144291000-144293400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:144291000-144294200	Weak transcription	Placenta	Placenta
37	chr6:144291000-144295000	Enhancers	Fetal Stomach	stomach
38	chr6:144291200-144294000	Weak transcription	Fetal Heart	heart
39	chr6:144291200-144294400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
40	chr6:144291200-144294600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:144291600-144294000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
42	chr6:144291800-144293200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
43	chr6:144291800-144293200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:144291800-144293400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:144291800-144293400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:144291800-144294000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
47	chr6:144292000-144293200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
48	chr6:144292000-144293800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr6:144292200-144292600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:144292400-144292800	Weak transcription	Fetal Muscle Leg	muscle

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