Variant report

Variant	rs9399508
Chromosome Location	chr6:145176175-145176176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11546879	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13195905	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs13198393	0.82[CHB][hapmap]
rs13202460	0.82[CHB][hapmap]
rs13204600	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13208243	0.91[MEX][hapmap]
rs13208561	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13210728	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs13212915	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13213382	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13218938	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1856418	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297844	0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2297845	1.00[ASW][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.80[EUR][1000 genomes]
rs2297846	0.85[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs35415004	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36083145	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4131501	0.81[CHB][hapmap]
rs4476850	0.82[JPT][hapmap];0.81[MEX][hapmap]
rs4495289	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4642498	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9321993	0.91[JPT][hapmap]
rs9373428	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs9373431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9376858	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs9390219	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9390240	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390242	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9399509	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399513	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9403603	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9403610	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs9403616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830833	chr6:145001310-145201143	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv886740	chr6:145105354-145199259	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9399508	PLAGL1	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145137400-145176800	Weak transcription	Fetal Heart	heart
2	chr6:145157800-145176400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:145158600-145176800	Weak transcription	Esophagus	oesophagus
4	chr6:145159200-145176600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:145159400-145177400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:145161000-145179000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr6:145162600-145176400	Weak transcription	Fetal Intestine Large	intestine
8	chr6:145162800-145176600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:145163800-145176200	Weak transcription	Fetal Intestine Small	intestine
10	chr6:145165800-145176600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:145166200-145176400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:145167200-145176800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:145167400-145188000	Weak transcription	NHDF-Ad	bronchial
14	chr6:145167800-145176800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:145168400-145177000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:145169200-145177200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:145169400-145189400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:145169600-145177200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:145169800-145177200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:145170400-145176400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:145170400-145177200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:145172000-145176800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:145172200-145176600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:145172200-145176600	Weak transcription	Aorta	Aorta
25	chr6:145172200-145176600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:145172200-145176600	Weak transcription	Spleen	Spleen
27	chr6:145172200-145177200	Weak transcription	HUVEC	blood vessel
28	chr6:145172400-145176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:145172400-145176600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr6:145172400-145176600	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:145172400-145177400	Weak transcription	Fetal Stomach	stomach
32	chr6:145172400-145178800	Weak transcription	Lung	lung
33	chr6:145172600-145177200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:145172800-145176200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:145172800-145176400	Weak transcription	Fetal Kidney	kidney
36	chr6:145173200-145176800	Weak transcription	NHLF	lung
37	chr6:145173400-145177200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr6:145173400-145177800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:145173400-145178600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr6:145173600-145178000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:145174000-145176400	Weak transcription	Liver	Liver
42	chr6:145174000-145177000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr6:145174600-145176400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:145175000-145176800	Weak transcription	Adipose Nuclei	Adipose
45	chr6:145175000-145177400	Weak transcription	Fetal Thymus	thymus
46	chr6:145175200-145176200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:145175200-145176600	Weak transcription	HSMM	muscle
48	chr6:145175200-145176800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:145175200-145177000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:145175200-145177000	Weak transcription	Dnd41	blood

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